diff --git a/config/config.go b/config/config.go
index 93d2ecd4d8..5b35e7a925 100644
--- a/config/config.go
+++ b/config/config.go
@@ -281,6 +281,11 @@ func resolveFilepaths(baseDir string, cfg *Config) {
 			consulcfg.TLSConfig.CertFile = join(consulcfg.TLSConfig.CertFile)
 			consulcfg.TLSConfig.KeyFile = join(consulcfg.TLSConfig.KeyFile)
 		}
+		for _, filecfg := range cfg.FileSDConfigs {
+			for i, fn := range filecfg.Files {
+				filecfg.Files[i] = join(fn)
+			}
+		}
 	}
 
 	for _, cfg := range cfg.ScrapeConfigs {
diff --git a/config/config_test.go b/config/config_test.go
index 0282deb0e5..2a5c53232a 100644
--- a/config/config_test.go
+++ b/config/config_test.go
@@ -104,11 +104,11 @@ var expectedConf = &Config{
 
 				FileSDConfigs: []*FileSDConfig{
 					{
-						Files:           []string{"foo/*.slow.json", "foo/*.slow.yml", "single/file.yml"},
+						Files:           []string{"testdata/foo/*.slow.json", "testdata/foo/*.slow.yml", "testdata/single/file.yml"},
 						RefreshInterval: model.Duration(10 * time.Minute),
 					},
 					{
-						Files:           []string{"bar/*.yaml"},
+						Files:           []string{"testdata/bar/*.yaml"},
 						RefreshInterval: model.Duration(5 * time.Minute),
 					},
 				},