diff --git a/tsdb/agent/db.go b/tsdb/agent/db.go
index 158bedc31b..4e53b6168b 100644
--- a/tsdb/agent/db.go
+++ b/tsdb/agent/db.go
@@ -631,17 +631,20 @@ Loop:
 	}
 }
 
-// keepSeriesInWALCheckpoint is used to determine whether a series record should be kept in the checkpoint
+// keepSeriesInWALCheckpointFn returns a function that is used to determine whether a series record should be kept in the checkpoint.
 // last is the last WAL segment that was considered for checkpointing.
-func (db *DB) keepSeriesInWALCheckpoint(id chunks.HeadSeriesRef, last int) bool {
-	// Keep the record if the series exists in the db.
-	if db.series.GetByID(id) != nil {
-		return true
-	}
+// NOTE: the agent implementation here is different from the Prometheus implementation, in that it uses WAL segment numbers instead of timestamps.
+func (db *DB) keepSeriesInWALCheckpointFn(last int) func(id chunks.HeadSeriesRef) bool {
+	return func(id chunks.HeadSeriesRef) bool {
+		// Keep the record if the series exists in the db.
+		if db.series.GetByID(id) != nil {
+			return true
+		}
 
-	// Keep the record if the series was recently deleted.
-	seg, ok := db.deleted[id]
-	return ok && seg > last
+		// Keep the record if the series was recently deleted.
+		seg, ok := db.deleted[id]
+		return ok && seg > last
+	}
 }
 
 func (db *DB) truncate(mint int64) error {
@@ -678,7 +681,7 @@ func (db *DB) truncate(mint int64) error {
 
 	db.metrics.checkpointCreationTotal.Inc()
 
-	if _, err = wlog.Checkpoint(db.logger, db.wal, first, last, db.keepSeriesInWALCheckpoint, mint); err != nil {
+	if _, err = wlog.Checkpoint(db.logger, db.wal, first, last, db.keepSeriesInWALCheckpointFn(last), mint); err != nil {
 		db.metrics.checkpointCreationFail.Inc()
 		var cerr *wlog.CorruptionErr
 		if errors.As(err, &cerr) {
diff --git a/tsdb/db_test.go b/tsdb/db_test.go
index 1b492a695e..87b3619705 100644
--- a/tsdb/db_test.go
+++ b/tsdb/db_test.go
@@ -1557,7 +1557,7 @@ func TestSizeRetention(t *testing.T) {
 	// Create a WAL checkpoint, and compare sizes.
 	first, last, err := wlog.Segments(db.Head().wal.Dir())
 	require.NoError(t, err)
-	_, err = wlog.Checkpoint(promslog.NewNopLogger(), db.Head().wal, first, last-1, func(chunks.HeadSeriesRef, int) bool { return false }, 0)
+	_, err = wlog.Checkpoint(promslog.NewNopLogger(), db.Head().wal, first, last-1, func(chunks.HeadSeriesRef) bool { return false }, 0)
 	require.NoError(t, err)
 	blockSize = int64(prom_testutil.ToFloat64(db.metrics.blocksBytes)) // Use the actual internal metrics.
 	walSize, err = db.Head().wal.Size()
@@ -4738,7 +4738,7 @@ func TestMetadataCheckpointingOnlyKeepsLatestEntry(t *testing.T) {
 	// Let's create a checkpoint.
 	first, last, err := wlog.Segments(w.Dir())
 	require.NoError(t, err)
-	keep := func(id chunks.HeadSeriesRef, _ int) bool {
+	keep := func(id chunks.HeadSeriesRef) bool {
 		return id != 3
 	}
 	_, err = wlog.Checkpoint(promslog.NewNopLogger(), w, first, last-1, keep, 0)
diff --git a/tsdb/head.go b/tsdb/head.go
index 20ab6e7731..cd0f771f96 100644
--- a/tsdb/head.go
+++ b/tsdb/head.go
@@ -110,7 +110,7 @@ type Head struct {
 	series *stripeSeries
 
 	walExpiriesMtx sync.Mutex
-	walExpiries    map[chunks.HeadSeriesRef]int // Series no longer in the head, and what WAL segment they must be kept until.
+	walExpiries    map[chunks.HeadSeriesRef]int64 // Series no longer in the head, and what time they must be kept until.
 
 	// TODO(codesome): Extend MemPostings to return only OOOPostings, Set OOOStatus, ... Like an additional map of ooo postings.
 	postings *index.MemPostings // Postings lists for terms.
@@ -337,7 +337,7 @@ func (h *Head) resetInMemoryState() error {
 	h.exemplars = es
 	h.postings = index.NewUnorderedMemPostings()
 	h.tombstones = tombstones.NewMemTombstones()
-	h.walExpiries = map[chunks.HeadSeriesRef]int{}
+	h.walExpiries = map[chunks.HeadSeriesRef]int64{}
 	h.chunkRange.Store(h.opts.ChunkRange)
 	h.minTime.Store(math.MaxInt64)
 	h.maxTime.Store(math.MinInt64)
@@ -791,7 +791,7 @@ func (h *Head) Init(minValidTime int64) error {
 
 		// A corrupted checkpoint is a hard error for now and requires user
 		// intervention. There's likely little data that can be recovered anyway.
-		if err := h.loadWAL(wlog.NewReader(sr), syms, multiRef, mmappedChunks, oooMmappedChunks, endAt); err != nil {
+		if err := h.loadWAL(wlog.NewReader(sr), syms, multiRef, mmappedChunks, oooMmappedChunks); err != nil {
 			return fmt.Errorf("backfill checkpoint: %w", err)
 		}
 		h.updateWALReplayStatusRead(startFrom)
@@ -825,7 +825,7 @@ func (h *Head) Init(minValidTime int64) error {
 		if err != nil {
 			return fmt.Errorf("segment reader (offset=%d): %w", offset, err)
 		}
-		err = h.loadWAL(wlog.NewReader(sr), syms, multiRef, mmappedChunks, oooMmappedChunks, endAt)
+		err = h.loadWAL(wlog.NewReader(sr), syms, multiRef, mmappedChunks, oooMmappedChunks)
 		if err := sr.Close(); err != nil {
 			h.logger.Warn("Error while closing the wal segments reader", "err", err)
 		}
@@ -1282,7 +1282,7 @@ func (h *Head) IsQuerierCollidingWithTruncation(querierMint, querierMaxt int64)
 	return false, false, 0
 }
 
-func (h *Head) getWALExpiry(id chunks.HeadSeriesRef) (int, bool) {
+func (h *Head) getWALExpiry(id chunks.HeadSeriesRef) (int64, bool) {
 	h.walExpiriesMtx.Lock()
 	defer h.walExpiriesMtx.Unlock()
 
@@ -1290,24 +1290,27 @@ func (h *Head) getWALExpiry(id chunks.HeadSeriesRef) (int, bool) {
 	return keepUntil, ok
 }
 
-func (h *Head) setWALExpiry(id chunks.HeadSeriesRef, keepUntil int) {
+// updateWALExpiry updates the WAL expiry for a series, keeping the higher of the current value and keepUntil.
+func (h *Head) updateWALExpiry(id chunks.HeadSeriesRef, keepUntil int64) {
 	h.walExpiriesMtx.Lock()
 	defer h.walExpiriesMtx.Unlock()
 
-	h.walExpiries[id] = keepUntil
+	h.walExpiries[id] = max(keepUntil, h.walExpiries[id])
 }
 
-// keepSeriesInWALCheckpoint is used to determine whether a series record should be kept in the checkpoint
-// last is the last WAL segment that was considered for checkpointing.
-func (h *Head) keepSeriesInWALCheckpoint(id chunks.HeadSeriesRef, last int) bool {
-	// Keep the record if the series exists in the head.
-	if h.series.getByID(id) != nil {
-		return true
-	}
+// keepSeriesInWALCheckpointFn returns a function that is used to determine whether a series record should be kept in the checkpoint.
+// mint is the time before which data in the WAL is being truncated.
+func (h *Head) keepSeriesInWALCheckpointFn(mint int64) func(id chunks.HeadSeriesRef) bool {
+	return func(id chunks.HeadSeriesRef) bool {
+		// Keep the record if the series exists in the head.
+		if h.series.getByID(id) != nil {
+			return true
+		}
 
-	// Keep the record if the series has an expiry set.
-	keepUntil, ok := h.getWALExpiry(id)
-	return ok && keepUntil > last
+		// Keep the record if the series has an expiry set.
+		keepUntil, ok := h.getWALExpiry(id)
+		return ok && keepUntil >= mint
+	}
 }
 
 // truncateWAL removes old data before mint from the WAL.
@@ -1344,7 +1347,7 @@ func (h *Head) truncateWAL(mint int64) error {
 	}
 
 	h.metrics.checkpointCreationTotal.Inc()
-	if _, err = wlog.Checkpoint(h.logger, h.wal, first, last, h.keepSeriesInWALCheckpoint, mint); err != nil {
+	if _, err = wlog.Checkpoint(h.logger, h.wal, first, last, h.keepSeriesInWALCheckpointFn(mint), mint); err != nil {
 		h.metrics.checkpointCreationFail.Inc()
 		var cerr *chunks.CorruptionErr
 		if errors.As(err, &cerr) {
@@ -1359,11 +1362,10 @@ func (h *Head) truncateWAL(mint int64) error {
 		h.logger.Error("truncating segments failed", "err", err)
 	}
 
-	// The checkpoint is written and segments before it is truncated, so stop
-	// tracking expired series.
+	// The checkpoint is written and data before mint is truncated, so stop tracking expired series.
 	h.walExpiriesMtx.Lock()
-	for ref, segment := range h.walExpiries {
-		if segment <= last {
+	for ref, keepUntil := range h.walExpiries {
+		if keepUntil < mint {
 			delete(h.walExpiries, ref)
 		}
 	}
@@ -1633,16 +1635,13 @@ func (h *Head) gc() (actualInOrderMint, minOOOTime int64, minMmapFile int) {
 	h.tombstones.TruncateBefore(mint)
 
 	if h.wal != nil {
-		_, last, _ := wlog.Segments(h.wal.Dir())
 		h.walExpiriesMtx.Lock()
-		// Keep series records until we're past segment 'last'
-		// because the WAL will still have samples records with
-		// this ref ID. If we didn't keep these series records then
-		// on start up when we replay the WAL, or any other code
-		// that reads the WAL, wouldn't be able to use those
-		// samples since we would have no labels for that ref ID.
+		// Samples for deleted series are likely still in the WAL, so flag that the deleted series records should be kept during
+		// WAL checkpointing while the WAL contains data through actualInOrderMint.
+		// If we didn't keep these series records then on start up when we replay the WAL, or any other code that reads the WAL,
+		// wouldn't be able to use those samples since we would have no labels for that ref ID.
 		for ref := range deleted {
-			h.walExpiries[chunks.HeadSeriesRef(ref)] = last
+			h.walExpiries[chunks.HeadSeriesRef(ref)] = actualInOrderMint
 		}
 		h.walExpiriesMtx.Unlock()
 	}
diff --git a/tsdb/head_test.go b/tsdb/head_test.go
index b4a238f685..e141c1dcfd 100644
--- a/tsdb/head_test.go
+++ b/tsdb/head_test.go
@@ -162,6 +162,10 @@ func populateTestWL(t testing.TB, w *wlog.WL, recs []interface{}, buf []byte) []
 			buf = enc.Tombstones(v, buf)
 		case []record.RefExemplar:
 			buf = enc.Exemplars(v, buf)
+		case []record.RefHistogramSample:
+			buf, _ = enc.HistogramSamples(v, buf)
+		case []record.RefFloatHistogramSample:
+			buf, _ = enc.FloatHistogramSamples(v, buf)
 		case []record.RefMmapMarker:
 			buf = enc.MmapMarkers(v, buf)
 		case []record.RefMetadata:
@@ -766,9 +770,7 @@ func TestHead_ReadWAL(t *testing.T) {
 			// But it should have a WAL expiry set.
 			keepUntil, ok := head.getWALExpiry(101)
 			require.True(t, ok)
-			_, last, err := wlog.Segments(w.Dir())
-			require.NoError(t, err)
-			require.Equal(t, last, keepUntil)
+			require.Equal(t, int64(101), keepUntil)
 			// Only the duplicate series record should have a WAL expiry set.
 			_, ok = head.getWALExpiry(50)
 			require.False(t, ok)
@@ -886,17 +888,265 @@ func TestHead_WALMultiRef(t *testing.T) {
 	}}, series)
 }
 
+func TestHead_WALCheckpointMultiRef(t *testing.T) {
+	cases := []struct {
+		name               string
+		walEntries         []interface{}
+		expectedWalExpiry  int64
+		walTruncateMinT    int64
+		expectedWalEntries []interface{}
+	}{
+		{
+			name: "Samples only; keep needed duplicate series record",
+			walEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefSample{
+					{Ref: 1, T: 100, V: 1},
+					{Ref: 2, T: 200, V: 2},
+					{Ref: 2, T: 500, V: 3},
+				},
+			},
+			expectedWalExpiry: 500,
+			walTruncateMinT:   500,
+			expectedWalEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefSample{
+					{Ref: 2, T: 500, V: 3},
+				},
+			},
+		},
+		{
+			name: "Tombstones only; keep needed duplicate series record",
+			walEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]tombstones.Stone{
+					{Ref: 1, Intervals: []tombstones.Interval{{Mint: 0, Maxt: 100}}},
+					{Ref: 2, Intervals: []tombstones.Interval{{Mint: 0, Maxt: 200}}},
+					{Ref: 2, Intervals: []tombstones.Interval{{Mint: 0, Maxt: 500}}},
+				},
+			},
+			expectedWalExpiry: 500,
+			walTruncateMinT:   500,
+			expectedWalEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]tombstones.Stone{
+					{Ref: 2, Intervals: []tombstones.Interval{{Mint: 0, Maxt: 500}}},
+				},
+			},
+		},
+		{
+			name: "Exemplars only; keep needed duplicate series record",
+			walEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefExemplar{
+					{Ref: 1, T: 100, V: 1, Labels: labels.FromStrings("trace_id", "asdf")},
+					{Ref: 2, T: 200, V: 2, Labels: labels.FromStrings("trace_id", "asdf")},
+					{Ref: 2, T: 500, V: 3, Labels: labels.FromStrings("trace_id", "asdf")},
+				},
+			},
+			expectedWalExpiry: 500,
+			walTruncateMinT:   500,
+			expectedWalEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefExemplar{
+					{Ref: 2, T: 500, V: 3, Labels: labels.FromStrings("trace_id", "asdf")},
+				},
+			},
+		},
+		{
+			name: "Histograms only; keep needed duplicate series record",
+			walEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefHistogramSample{
+					{Ref: 1, T: 100, H: &histogram.Histogram{}},
+					{Ref: 2, T: 200, H: &histogram.Histogram{}},
+					{Ref: 2, T: 500, H: &histogram.Histogram{}},
+				},
+			},
+			expectedWalExpiry: 500,
+			walTruncateMinT:   500,
+			expectedWalEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefHistogramSample{
+					{Ref: 2, T: 500, H: &histogram.Histogram{}},
+				},
+			},
+		},
+		{
+			name: "Float histograms only; keep needed duplicate series record",
+			walEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefFloatHistogramSample{
+					{Ref: 1, T: 100, FH: &histogram.FloatHistogram{}},
+					{Ref: 2, T: 200, FH: &histogram.FloatHistogram{}},
+					{Ref: 2, T: 500, FH: &histogram.FloatHistogram{}},
+				},
+			},
+			expectedWalExpiry: 500,
+			walTruncateMinT:   500,
+			expectedWalEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefFloatHistogramSample{
+					{Ref: 2, T: 500, FH: &histogram.FloatHistogram{}},
+				},
+			},
+		},
+		{
+			name: "All record types; keep needed duplicate series record until last record",
+			// Series with 2 refs and samples for both
+			walEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefSample{
+					{Ref: 2, T: 500, V: 3},
+				},
+				[]tombstones.Stone{
+					{Ref: 2, Intervals: []tombstones.Interval{{Mint: 0, Maxt: 500}}},
+				},
+				[]record.RefExemplar{
+					{Ref: 2, T: 800, V: 2, Labels: labels.FromStrings("trace_id", "asdf")},
+				},
+				[]record.RefHistogramSample{
+					{Ref: 2, T: 500, H: &histogram.Histogram{}},
+				},
+				[]record.RefFloatHistogramSample{
+					{Ref: 2, T: 500, FH: &histogram.FloatHistogram{}},
+				},
+			},
+			expectedWalExpiry: 800,
+			walTruncateMinT:   700,
+			expectedWalEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefExemplar{
+					{Ref: 2, T: 800, V: 2, Labels: labels.FromStrings("trace_id", "asdf")},
+				},
+			},
+		},
+		{
+			name: "All record types; drop expired duplicate series record",
+			// Series with 2 refs and samples for both
+			walEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+					{Ref: 2, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefSample{
+					{Ref: 2, T: 500, V: 2},
+					{Ref: 1, T: 900, V: 3},
+				},
+				[]tombstones.Stone{
+					{Ref: 2, Intervals: []tombstones.Interval{{Mint: 0, Maxt: 750}}},
+				},
+				[]record.RefExemplar{
+					{Ref: 2, T: 800, V: 2, Labels: labels.FromStrings("trace_id", "asdf")},
+				},
+				[]record.RefHistogramSample{
+					{Ref: 2, T: 600, H: &histogram.Histogram{}},
+				},
+				[]record.RefFloatHistogramSample{
+					{Ref: 2, T: 700, FH: &histogram.FloatHistogram{}},
+				},
+			},
+			expectedWalExpiry: 800,
+			walTruncateMinT:   900,
+			expectedWalEntries: []interface{}{
+				[]record.RefSeries{
+					{Ref: 1, Labels: labels.FromStrings("a", "1")},
+				},
+				[]record.RefSample{
+					{Ref: 1, T: 900, V: 3},
+				},
+			},
+		},
+	}
+
+	for _, tc := range cases {
+		t.Run(tc.name, func(t *testing.T) {
+			h, w := newTestHead(t, 1000, compression.None, false)
+			t.Cleanup(func() {
+				require.NoError(t, h.Close())
+			})
+
+			populateTestWL(t, w, tc.walEntries, nil)
+			first, _, err := wlog.Segments(w.Dir())
+			require.NoError(t, err)
+
+			require.NoError(t, h.Init(0))
+
+			keepUntil, ok := h.getWALExpiry(2)
+			require.True(t, ok)
+			require.Equal(t, tc.expectedWalExpiry, keepUntil)
+
+			// Each truncation creates a new segment, so attempt truncations until a checkpoint is created
+			for {
+				h.lastWALTruncationTime.Store(0) // Reset so that it's always time to truncate the WAL
+				err := h.truncateWAL(tc.walTruncateMinT)
+				require.NoError(t, err)
+				f, _, err := wlog.Segments(w.Dir())
+				require.NoError(t, err)
+				if f > first {
+					break
+				}
+			}
+
+			// Read test WAL , checkpoint first
+			checkpointDir, _, err := wlog.LastCheckpoint(w.Dir())
+			require.NoError(t, err)
+			cprecs := readTestWAL(t, checkpointDir)
+			recs := readTestWAL(t, w.Dir())
+			recs = append(cprecs, recs...)
+
+			// Use testutil.RequireEqual which handles labels properly with dedupelabels
+			testutil.RequireEqual(t, tc.expectedWalEntries, recs)
+		})
+	}
+}
+
 func TestHead_KeepSeriesInWALCheckpoint(t *testing.T) {
 	existingRef := 1
 	existingLbls := labels.FromStrings("foo", "bar")
-	deletedKeepUntil := 10
+	keepUntil := int64(10)
 
 	cases := []struct {
-		name      string
-		prepare   func(t *testing.T, h *Head)
-		seriesRef chunks.HeadSeriesRef
-		last      int
-		expected  bool
+		name     string
+		prepare  func(t *testing.T, h *Head)
+		mint     int64
+		expected bool
 	}{
 		{
 			name: "keep series still in the head",
@@ -904,26 +1154,22 @@ func TestHead_KeepSeriesInWALCheckpoint(t *testing.T) {
 				_, _, err := h.getOrCreateWithID(chunks.HeadSeriesRef(existingRef), existingLbls.Hash(), existingLbls, false)
 				require.NoError(t, err)
 			},
-			seriesRef: chunks.HeadSeriesRef(existingRef),
-			expected:  true,
+			expected: true,
 		},
 		{
-			name: "keep deleted series with keepUntil > last",
-			prepare: func(_ *testing.T, h *Head) {
-				h.setWALExpiry(chunks.HeadSeriesRef(existingRef), deletedKeepUntil)
-			},
-			seriesRef: chunks.HeadSeriesRef(existingRef),
-			last:      deletedKeepUntil - 1,
-			expected:  true,
+			name:     "keep series with keepUntil > mint",
+			mint:     keepUntil - 1,
+			expected: true,
 		},
 		{
-			name: "drop deleted series with keepUntil <= last",
-			prepare: func(_ *testing.T, h *Head) {
-				h.setWALExpiry(chunks.HeadSeriesRef(existingRef), deletedKeepUntil)
-			},
-			seriesRef: chunks.HeadSeriesRef(existingRef),
-			last:      deletedKeepUntil,
-			expected:  false,
+			name:     "keep series with keepUntil = mint",
+			mint:     keepUntil,
+			expected: true,
+		},
+		{
+			name:     "drop series with keepUntil < mint",
+			mint:     keepUntil + 1,
+			expected: false,
 		},
 	}
 
@@ -936,10 +1182,12 @@ func TestHead_KeepSeriesInWALCheckpoint(t *testing.T) {
 
 			if tc.prepare != nil {
 				tc.prepare(t, h)
+			} else {
+				h.updateWALExpiry(chunks.HeadSeriesRef(existingRef), keepUntil)
 			}
 
-			kept := h.keepSeriesInWALCheckpoint(tc.seriesRef, tc.last)
-			require.Equal(t, tc.expected, kept)
+			keep := h.keepSeriesInWALCheckpointFn(tc.mint)
+			require.Equal(t, tc.expected, keep(chunks.HeadSeriesRef(existingRef)))
 		})
 	}
 }
diff --git a/tsdb/head_wal.go b/tsdb/head_wal.go
index 3e0dadb526..9b0982423f 100644
--- a/tsdb/head_wal.go
+++ b/tsdb/head_wal.go
@@ -76,7 +76,7 @@ func counterAddNonZero(v *prometheus.CounterVec, value float64, lvs ...string) {
 	}
 }
 
-func (h *Head) loadWAL(r *wlog.Reader, syms *labels.SymbolTable, multiRef map[chunks.HeadSeriesRef]chunks.HeadSeriesRef, mmappedChunks, oooMmappedChunks map[chunks.HeadSeriesRef][]*mmappedChunk, lastSegment int) (err error) {
+func (h *Head) loadWAL(r *wlog.Reader, syms *labels.SymbolTable, multiRef map[chunks.HeadSeriesRef]chunks.HeadSeriesRef, mmappedChunks, oooMmappedChunks map[chunks.HeadSeriesRef][]*mmappedChunk) (err error) {
 	// Track number of missing series records that were referenced by other records.
 	unknownSeriesRefs := &seriesRefSet{refs: make(map[chunks.HeadSeriesRef]struct{}), mtx: sync.Mutex{}}
 	// Track number of different records that referenced a series we don't know about
@@ -266,8 +266,6 @@ Outer:
 				}
 				if !created {
 					multiRef[walSeries.Ref] = mSeries.ref
-					// Set the WAL expiry for the duplicate series, so it is kept in subsequent WAL checkpoints.
-					h.setWALExpiry(walSeries.Ref, lastSegment)
 				}
 
 				idx := uint64(mSeries.ref) % uint64(concurrency)
@@ -293,6 +291,8 @@ Outer:
 						continue // Before minValidTime: discard.
 					}
 					if r, ok := multiRef[sam.Ref]; ok {
+						// This is a sample for a duplicate series, so we need to keep the series record at least until this record's timestamp.
+						h.updateWALExpiry(sam.Ref, sam.T)
 						sam.Ref = r
 					}
 					mod := uint64(sam.Ref) % uint64(concurrency)
@@ -314,6 +314,8 @@ Outer:
 						continue
 					}
 					if r, ok := multiRef[chunks.HeadSeriesRef(s.Ref)]; ok {
+						// This is a tombstone for a duplicate series, so we need to keep the series record at least until this record's timestamp.
+						h.updateWALExpiry(chunks.HeadSeriesRef(s.Ref), itv.Maxt)
 						s.Ref = storage.SeriesRef(r)
 					}
 					if m := h.series.getByID(chunks.HeadSeriesRef(s.Ref)); m == nil {
@@ -331,6 +333,8 @@ Outer:
 					continue
 				}
 				if r, ok := multiRef[e.Ref]; ok {
+					// This is an exemplar for a duplicate series, so we need to keep the series record at least until this record's timestamp.
+					h.updateWALExpiry(e.Ref, e.T)
 					e.Ref = r
 				}
 				exemplarsInput <- e
@@ -355,6 +359,8 @@ Outer:
 						continue // Before minValidTime: discard.
 					}
 					if r, ok := multiRef[sam.Ref]; ok {
+						// This is a histogram sample for a duplicate series, so we need to keep the series record at least until this record's timestamp.
+						h.updateWALExpiry(sam.Ref, sam.T)
 						sam.Ref = r
 					}
 					mod := uint64(sam.Ref) % uint64(concurrency)
@@ -388,6 +394,8 @@ Outer:
 						continue // Before minValidTime: discard.
 					}
 					if r, ok := multiRef[sam.Ref]; ok {
+						// This is a float histogram sample for a duplicate series, so we need to keep the series record at least until this record's timestamp.
+						h.updateWALExpiry(sam.Ref, sam.T)
 						sam.Ref = r
 					}
 					mod := uint64(sam.Ref) % uint64(concurrency)
diff --git a/tsdb/wlog/checkpoint.go b/tsdb/wlog/checkpoint.go
index 2c1b0c0534..5c607d7030 100644
--- a/tsdb/wlog/checkpoint.go
+++ b/tsdb/wlog/checkpoint.go
@@ -93,7 +93,7 @@ const CheckpointPrefix = "checkpoint."
 // segmented format as the original WAL itself.
 // This makes it easy to read it through the WAL package and concatenate
 // it with the original WAL.
-func Checkpoint(logger *slog.Logger, w *WL, from, to int, keep func(id chunks.HeadSeriesRef, last int) bool, mint int64) (*CheckpointStats, error) {
+func Checkpoint(logger *slog.Logger, w *WL, from, to int, keep func(id chunks.HeadSeriesRef) bool, mint int64) (*CheckpointStats, error) {
 	stats := &CheckpointStats{}
 	var sgmReader io.ReadCloser
 
@@ -181,7 +181,7 @@ func Checkpoint(logger *slog.Logger, w *WL, from, to int, keep func(id chunks.He
 			// Drop irrelevant series in place.
 			repl := series[:0]
 			for _, s := range series {
-				if keep(s.Ref, to) {
+				if keep(s.Ref) {
 					repl = append(repl, s)
 				}
 			}
@@ -323,7 +323,7 @@ func Checkpoint(logger *slog.Logger, w *WL, from, to int, keep func(id chunks.He
 			// Only keep reference to the latest found metadata for each refID.
 			repl := 0
 			for _, m := range metadata {
-				if keep(m.Ref, to) {
+				if keep(m.Ref) {
 					if _, ok := latestMetadataMap[m.Ref]; !ok {
 						repl++
 					}
diff --git a/tsdb/wlog/checkpoint_test.go b/tsdb/wlog/checkpoint_test.go
index 90c1035229..0b0d11ac45 100644
--- a/tsdb/wlog/checkpoint_test.go
+++ b/tsdb/wlog/checkpoint_test.go
@@ -292,7 +292,7 @@ func TestCheckpoint(t *testing.T) {
 			}
 			require.NoError(t, w.Close())
 
-			stats, err := Checkpoint(promslog.NewNopLogger(), w, 100, 106, func(x chunks.HeadSeriesRef, _ int) bool {
+			stats, err := Checkpoint(promslog.NewNopLogger(), w, 100, 106, func(x chunks.HeadSeriesRef) bool {
 				return x%2 == 0
 			}, last/2)
 			require.NoError(t, err)
diff --git a/tsdb/wlog/watcher_test.go b/tsdb/wlog/watcher_test.go
index 4b8b408edc..57a4bbe401 100644
--- a/tsdb/wlog/watcher_test.go
+++ b/tsdb/wlog/watcher_test.go
@@ -400,7 +400,7 @@ func TestReadToEndWithCheckpoint(t *testing.T) {
 				}
 			}
 
-			Checkpoint(promslog.NewNopLogger(), w, 0, 1, func(chunks.HeadSeriesRef, int) bool { return true }, 0)
+			Checkpoint(promslog.NewNopLogger(), w, 0, 1, func(chunks.HeadSeriesRef) bool { return true }, 0)
 			w.Truncate(1)
 
 			// Write more records after checkpointing.
@@ -492,7 +492,7 @@ func TestReadCheckpoint(t *testing.T) {
 			}
 			_, err = w.NextSegmentSync()
 			require.NoError(t, err)
-			_, err = Checkpoint(promslog.NewNopLogger(), w, 30, 31, func(chunks.HeadSeriesRef, int) bool { return true }, 0)
+			_, err = Checkpoint(promslog.NewNopLogger(), w, 30, 31, func(chunks.HeadSeriesRef) bool { return true }, 0)
 			require.NoError(t, err)
 			require.NoError(t, w.Truncate(32))
 
@@ -655,7 +655,7 @@ func TestCheckpointSeriesReset(t *testing.T) {
 				return wt.checkNumSeries() == seriesCount
 			}, 10*time.Second, 1*time.Second)
 
-			_, err = Checkpoint(promslog.NewNopLogger(), w, 2, 4, func(chunks.HeadSeriesRef, int) bool { return true }, 0)
+			_, err = Checkpoint(promslog.NewNopLogger(), w, 2, 4, func(chunks.HeadSeriesRef) bool { return true }, 0)
 			require.NoError(t, err)
 
 			err = w.Truncate(5)