diff --git a/test/unit-tests/HtmlUtils-test.tsx b/test/unit-tests/HtmlUtils-test.tsx
index 0650db1890..16546e69dc 100644
--- a/test/unit-tests/HtmlUtils-test.tsx
+++ b/test/unit-tests/HtmlUtils-test.tsx
@@ -7,22 +7,19 @@ Please see LICENSE files in the repository root for full details.
 */
 
 import React from "react";
-import { mocked } from "jest-mock";
 import { render, screen } from "jest-matrix-react";
 import parse from "html-react-parser";
 
 import { bodyToHtml, bodyToNode, formatEmojis, topicToHtml } from "../../src/HtmlUtils";
 import SettingsStore from "../../src/settings/SettingsStore";
-
-jest.mock("../../src/settings/SettingsStore");
-
-const enableHtmlTopicFeature = () => {
-    mocked(SettingsStore).getValue.mockImplementation((arg): any => {
-        return arg === "feature_html_topic";
-    });
-};
+import { SettingLevel } from "../../src/settings/SettingLevel";
+import SdkConfig from "../../src/SdkConfig";
 
 describe("topicToHtml", () => {
+    afterEach(() => {
+        SettingsStore.reset();
+    });
+
     function getContent() {
         return screen.getByRole("contentinfo").children[0].innerHTML;
     }
@@ -38,19 +35,19 @@ describe("topicToHtml", () => {
     });
 
     it("converts literal HTML topic to HTML", async () => {
-        enableHtmlTopicFeature();
+        SettingsStore.setValue("feature_html_topic", null, SettingLevel.DEVICE, true);
         render(<div role="contentinfo">{topicToHtml("<b>pizza</b>", undefined, null, false)}</div>);
         expect(getContent()).toEqual("&lt;b&gt;pizza&lt;/b&gt;");
     });
 
     it("converts true HTML topic to HTML", async () => {
-        enableHtmlTopicFeature();
+        SettingsStore.setValue("feature_html_topic", null, SettingLevel.DEVICE, true);
         render(<div role="contentinfo">{topicToHtml("**pizza**", "<b>pizza</b>", null, false)}</div>);
         expect(getContent()).toEqual("<b>pizza</b>");
     });
 
     it("converts true HTML topic with emoji to HTML", async () => {
-        enableHtmlTopicFeature();
+        SettingsStore.setValue("feature_html_topic", null, SettingLevel.DEVICE, true);
         render(<div role="contentinfo">{topicToHtml("**pizza** 🍕", "<b>pizza</b> 🍕", null, false)}</div>);
         expect(getContent()).toEqual('<b>pizza</b> <span class="mx_Emoji" title=":pizza:">🍕</span>');
     });
@@ -107,7 +104,12 @@ describe("bodyToHtml", () => {
 
     describe("feature_latex_maths", () => {
         beforeEach(() => {
-            jest.spyOn(SettingsStore, "getValue").mockImplementation((feature) => feature === "feature_latex_maths");
+            SettingsStore.setValue("feature_latex_maths", null, SettingLevel.DEVICE, true);
+        });
+
+        afterEach(() => {
+            SettingsStore.reset();
+            SdkConfig.reset();
         });
 
         it("should render inline katex", () => {
@@ -228,4 +230,8 @@ describe("bodyToNode", () => {
 
         expect(asFragment()).toMatchSnapshot();
     });
+
+    afterEach(() => {
+        jest.resetAllMocks();
+    });
 });
diff --git a/test/unit-tests/components/structures/MatrixChat-test.tsx b/test/unit-tests/components/structures/MatrixChat-test.tsx
index d6db2ce941..8633b3cfcf 100644
--- a/test/unit-tests/components/structures/MatrixChat-test.tsx
+++ b/test/unit-tests/components/structures/MatrixChat-test.tsx
@@ -484,6 +484,10 @@ describe("<MatrixChat />", () => {
                 );
             });
 
+            afterEach(() => {
+                SettingsStore.reset();
+            });
+
             it("should persist login credentials", async () => {
                 getComponent({ realQueryParams });
 
diff --git a/test/unit-tests/components/structures/TimelinePanel-test.tsx b/test/unit-tests/components/structures/TimelinePanel-test.tsx
index 886fe777e4..87c788d9f9 100644
--- a/test/unit-tests/components/structures/TimelinePanel-test.tsx
+++ b/test/unit-tests/components/structures/TimelinePanel-test.tsx
@@ -50,6 +50,8 @@ import SettingsStore from "../../../../src/settings/SettingsStore";
 import ScrollPanel from "../../../../src/components/structures/ScrollPanel";
 import defaultDispatcher from "../../../../src/dispatcher/dispatcher";
 import { Action } from "../../../../src/dispatcher/actions";
+import { SettingLevel } from "../../../../src/settings/SettingLevel";
+import MatrixClientBackedController from "../../../../src/settings/controllers/MatrixClientBackedController";
 
 // ScrollPanel calls this, but jsdom doesn't mock it for us
 HTMLDivElement.prototype.scrollBy = () => {};
@@ -310,18 +312,14 @@ describe("TimelinePanel", () => {
 
             describe("and sending receipts is disabled", () => {
                 beforeEach(async () => {
-                    client.isVersionSupported.mockResolvedValue(true);
-                    client.doesServerSupportUnstableFeature.mockResolvedValue(true);
-
-                    jest.spyOn(SettingsStore, "getValue").mockImplementation((setting: string): any => {
-                        if (setting === "sendReadReceipts") return false;
-
-                        return undefined;
-                    });
+                    // Ensure this setting is supported, otherwise it will use the default value.
+                    client.isVersionSupported.mockImplementation(async (v) => v === "v1.4");
+                    MatrixClientBackedController.matrixClient = client;
+                    SettingsStore.setValue("sendReadReceipts", null, SettingLevel.DEVICE, false);
                 });
 
                 afterEach(() => {
-                    mocked(SettingsStore.getValue).mockReset();
+                    SettingsStore.reset();
                 });
 
                 it("should send a fully read marker and a private receipt", async () => {
diff --git a/test/unit-tests/components/views/rooms/RoomHeader/RoomHeader-test.tsx b/test/unit-tests/components/views/rooms/RoomHeader/RoomHeader-test.tsx
index 846adc8ab4..17d1a048c2 100644
--- a/test/unit-tests/components/views/rooms/RoomHeader/RoomHeader-test.tsx
+++ b/test/unit-tests/components/views/rooms/RoomHeader/RoomHeader-test.tsx
@@ -1,5 +1,5 @@
 /*
-Copyright 2024 New Vector Ltd.
+Copyright 2024, 2025 New Vector Ltd.
 Copyright 2023 The Matrix.org Foundation C.I.C.
 
 SPDX-License-Identifier: AGPL-3.0-only OR GPL-3.0-only OR LicenseRef-Element-Commercial
@@ -57,6 +57,7 @@ import * as UseCall from "../../../../../../src/hooks/useCall";
 import { SdkContextClass } from "../../../../../../src/contexts/SDKContext";
 import WidgetStore, { type IApp } from "../../../../../../src/stores/WidgetStore";
 import { UIFeature } from "../../../../../../src/settings/UIFeature";
+import { SettingLevel } from "../../../../../../src/settings/SettingLevel";
 
 jest.mock("../../../../../../src/utils/ShieldUtils");
 jest.mock("../../../../../../src/hooks/right-panel/useCurrentPhase", () => ({
@@ -99,6 +100,7 @@ describe("RoomHeader", () => {
 
     afterEach(() => {
         jest.restoreAllMocks();
+        SettingsStore.reset();
     });
 
     it("renders the room header", () => {
@@ -187,9 +189,7 @@ describe("RoomHeader", () => {
 
     it("opens the notifications panel", async () => {
         const user = userEvent.setup();
-        jest.spyOn(SettingsStore, "getValue").mockImplementation((name: string): any => {
-            if (name === "feature_notifications") return true;
-        });
+        SettingsStore.setValue("feature_notifications", null, SettingLevel.DEVICE, true);
 
         render(<RoomHeader room={room} />, getWrapper());
 
@@ -228,7 +228,15 @@ describe("RoomHeader", () => {
 
     describe("UIFeature.Widgets enabled (default)", () => {
         beforeEach(() => {
-            jest.spyOn(SettingsStore, "getValue").mockImplementation((feature) => feature == UIFeature.Widgets);
+            SdkConfig.put({
+                setting_defaults: {
+                    [UIFeature.Widgets]: true,
+                },
+            });
+        });
+
+        afterEach(() => {
+            SdkConfig.reset();
         });
 
         it("should show call buttons in a room with 2 members", () => {
@@ -248,7 +256,15 @@ describe("RoomHeader", () => {
 
     describe("UIFeature.Widgets disabled", () => {
         beforeEach(() => {
-            jest.spyOn(SettingsStore, "getValue").mockImplementation((feature) => false);
+            SdkConfig.put({
+                setting_defaults: {
+                    [UIFeature.Widgets]: false,
+                },
+            });
+        });
+
+        afterEach(() => {
+            SdkConfig.reset();
         });
 
         it("should show call buttons in a room with 2 members", () => {
@@ -268,7 +284,15 @@ describe("RoomHeader", () => {
 
     describe("groups call disabled", () => {
         beforeEach(() => {
-            jest.spyOn(SettingsStore, "getValue").mockImplementation((feature) => feature == UIFeature.Widgets);
+            SdkConfig.put({
+                setting_defaults: {
+                    [UIFeature.Widgets]: true,
+                },
+            });
+        });
+
+        afterEach(() => {
+            SdkConfig.reset();
         });
 
         it("you can't call if you're alone", () => {
@@ -333,15 +357,26 @@ describe("RoomHeader", () => {
 
     describe("group call enabled", () => {
         beforeEach(() => {
-            jest.spyOn(SettingsStore, "getValue").mockImplementation(
-                (feature) => feature === "feature_group_calls" || feature == UIFeature.Widgets,
-            );
+            SdkConfig.put({
+                features: {
+                    feature_group_calls: true,
+                },
+            });
+        });
+
+        afterEach(() => {
+            SdkConfig.reset();
+            jest.restoreAllMocks();
         });
 
         it("renders only the video call element", async () => {
             const user = userEvent.setup();
             mockRoomMembers(room, 3);
-            jest.spyOn(SdkConfig, "get").mockReturnValue({ use_exclusively: true });
+            SdkConfig.add({
+                element_call: {
+                    use_exclusively: true,
+                },
+            });
             // allow element calls
             jest.spyOn(room.currentState, "mayClientSendStateEvent").mockReturnValue(true);
 
@@ -359,7 +394,11 @@ describe("RoomHeader", () => {
         });
 
         it("can't call if there's an ongoing (pinned) call", () => {
-            jest.spyOn(SdkConfig, "get").mockReturnValue({ use_exclusively: true });
+            SdkConfig.add({
+                element_call: {
+                    use_exclusively: true,
+                },
+            });
             // allow element calls
             jest.spyOn(room.currentState, "mayClientSendStateEvent").mockReturnValue(true);
             jest.spyOn(WidgetLayoutStore.instance, "isInContainer").mockReturnValue(true);
@@ -377,7 +416,14 @@ describe("RoomHeader", () => {
         it("clicking on ongoing (unpinned) call re-pins it", async () => {
             const user = userEvent.setup();
             mockRoomMembers(room, 3);
-            jest.spyOn(SettingsStore, "getValue").mockImplementation((feature) => feature == UIFeature.Widgets);
+            SdkConfig.add({
+                setting_defaults: {
+                    [UIFeature.Widgets]: true,
+                },
+                features: {
+                    feature_group_calls: false,
+                },
+            });
             // allow calls
             jest.spyOn(room.currentState, "mayClientSendStateEvent").mockReturnValue(true);
             jest.spyOn(WidgetLayoutStore.instance, "isInContainer").mockReturnValue(false);
@@ -427,8 +473,10 @@ describe("RoomHeader", () => {
             jest.spyOn(room.currentState, "maySendStateEvent").mockReturnValue(true);
             jest.spyOn(room, "getJoinRule").mockReturnValue(JoinRule.Invite);
             jest.spyOn(room, "canInvite").mockReturnValue(false);
-            const guestSpaUrlMock = jest.spyOn(SdkConfig, "get").mockImplementation((key) => {
-                return { guest_spa_url: "https://guest_spa_url.com", url: "https://spa_url.com" };
+            SdkConfig.add({
+                element_call: {
+                    guest_spa_url: "https://guest_spa_url.com",
+                },
             });
             const { container: containerNoInviteNotPublicCanUpgradeAccess } = render(
                 <RoomHeader room={room} />,
@@ -442,8 +490,10 @@ describe("RoomHeader", () => {
             jest.spyOn(room.currentState, "maySendStateEvent").mockReturnValue(false);
             jest.spyOn(room, "getJoinRule").mockReturnValue(JoinRule.Invite);
             jest.spyOn(room, "canInvite").mockReturnValue(false);
-            jest.spyOn(SdkConfig, "get").mockImplementation((key) => {
-                return { guest_spa_url: "https://guest_spa_url.com", url: "https://spa_url.com" };
+            SdkConfig.add({
+                element_call: {
+                    guest_spa_url: "https://guest_spa_url.com",
+                },
             });
             const { container: containerNoInviteNotPublic } = render(<RoomHeader room={room} />, getWrapper());
             expect(queryAllByLabelText(containerNoInviteNotPublic, "There's no one here to call")).toHaveLength(2);
@@ -463,8 +513,9 @@ describe("RoomHeader", () => {
             const { container: containerInvitePublic } = render(<RoomHeader room={room} />, getWrapper());
             expect(queryAllByLabelText(containerInvitePublic, "There's no one here to call")).toHaveLength(0);
 
+            // Clear guest_spa_url
+            SdkConfig.reset();
             // last we can allow everything but without guest_spa_url nothing will work
-            guestSpaUrlMock.mockRestore();
             const { container: containerAllAllowedButNoGuestSpaUrl } = render(<RoomHeader room={room} />, getWrapper());
             expect(
                 queryAllByLabelText(containerAllAllowedButNoGuestSpaUrl, "There's no one here to call"),
@@ -643,6 +694,10 @@ describe("RoomHeader", () => {
             ]);
         });
 
+        afterEach(() => {
+            SdkConfig.reset();
+        });
+
         it.each([
             [ShieldUtils.E2EStatus.Verified, "Verified"],
             [ShieldUtils.E2EStatus.Warning, "Untrusted"],
@@ -655,6 +710,11 @@ describe("RoomHeader", () => {
         });
 
         it("does not show the face pile for DMs", () => {
+            SdkConfig.put({
+                features: {
+                    feature_notifications: false,
+                },
+            });
             const { asFragment } = render(<RoomHeader room={room} />, getWrapper());
 
             expect(asFragment()).toMatchSnapshot();
@@ -751,7 +811,7 @@ describe("RoomHeader", () => {
 
     describe("ask to join enabled", () => {
         it("does render the RoomKnocksBar", () => {
-            jest.spyOn(SettingsStore, "getValue").mockImplementation((feature) => feature === "feature_ask_to_join");
+            SettingsStore.setValue("feature_ask_to_join", null, SettingLevel.DEVICE, true);
             jest.spyOn(room, "canInvite").mockReturnValue(true);
             jest.spyOn(room, "getJoinRule").mockReturnValue(JoinRule.Knock);
             jest.spyOn(room, "getMembersWithMembership").mockReturnValue([new RoomMember(room.roomId, "@foo")]);
diff --git a/test/unit-tests/components/views/rooms/RoomHeader/__snapshots__/RoomHeader-test.tsx.snap b/test/unit-tests/components/views/rooms/RoomHeader/__snapshots__/RoomHeader-test.tsx.snap
index b0505fac0b..bbcf4cfb4b 100644
--- a/test/unit-tests/components/views/rooms/RoomHeader/__snapshots__/RoomHeader-test.tsx.snap
+++ b/test/unit-tests/components/views/rooms/RoomHeader/__snapshots__/RoomHeader-test.tsx.snap
@@ -55,7 +55,7 @@ exports[`RoomHeader dm does not show the face pile for DMs 1`] = `
         style="--cpd-icon-button-size: 100%; --cpd-color-icon-tertiary: var(--cpd-color-icon-disabled);"
       >
         <svg
-          aria-labelledby=":r15i:"
+          aria-labelledby=":r1c8:"
           fill="currentColor"
           height="1em"
           viewBox="0 0 24 24"
@@ -71,7 +71,7 @@ exports[`RoomHeader dm does not show the face pile for DMs 1`] = `
     <button
       aria-disabled="true"
       aria-label="There's no one here to call"
-      aria-labelledby=":r15n:"
+      aria-labelledby=":r1cd:"
       class="_icon-button_m2erp_8"
       role="button"
       style="--cpd-icon-button-size: 32px;"
@@ -96,7 +96,7 @@ exports[`RoomHeader dm does not show the face pile for DMs 1`] = `
     </button>
     <button
       aria-label="Threads"
-      aria-labelledby=":r15s:"
+      aria-labelledby=":r1ci:"
       class="_icon-button_m2erp_8"
       role="button"
       style="--cpd-icon-button-size: 32px;"
@@ -122,7 +122,7 @@ exports[`RoomHeader dm does not show the face pile for DMs 1`] = `
     </button>
     <button
       aria-label="Room info"
-      aria-labelledby=":r161:"
+      aria-labelledby=":r1cn:"
       class="_icon-button_m2erp_8"
       role="button"
       style="--cpd-icon-button-size: 32px;"
diff --git a/test/unit-tests/components/views/settings/tabs/room/NotificationSettingsTab-test.tsx b/test/unit-tests/components/views/settings/tabs/room/NotificationSettingsTab-test.tsx
index 54d8bd7ac0..f4efc39e1f 100644
--- a/test/unit-tests/components/views/settings/tabs/room/NotificationSettingsTab-test.tsx
+++ b/test/unit-tests/components/views/settings/tabs/room/NotificationSettingsTab-test.tsx
@@ -37,6 +37,10 @@ describe("NotificatinSettingsTab", () => {
         NotificationSettingsTab.contextType = React.createContext<MatrixClient>(cli);
     });
 
+    afterEach(() => {
+        SettingsStore.reset();
+    });
+
     it("should prevent »Settings« link click from bubbling up to radio buttons", async () => {
         const tab = renderTab();
 
diff --git a/test/unit-tests/utils/notifications-test.ts b/test/unit-tests/utils/notifications-test.ts
index 2a761f7670..5a416deede 100644
--- a/test/unit-tests/utils/notifications-test.ts
+++ b/test/unit-tests/utils/notifications-test.ts
@@ -1,5 +1,5 @@
 /*
-Copyright 2024 New Vector Ltd.
+Copyright 2024, 2025 New Vector Ltd.
 Copyright 2022 The Matrix.org Foundation C.I.C.
 
 SPDX-License-Identifier: AGPL-3.0-only OR GPL-3.0-only OR LicenseRef-Element-Commercial
@@ -28,13 +28,13 @@ import {
     getMarkedUnreadState,
     setMarkedUnreadState,
 } from "../../../src/utils/notifications";
-import SettingsStore from "../../../src/settings/SettingsStore";
-import { getMockClientWithEventEmitter } from "../../test-utils/client";
+import { getMockClientWithEventEmitter, mockClientMethodsServer } from "../../test-utils/client";
 import { mkMessage, stubClient } from "../../test-utils/test-utils";
 import { MatrixClientPeg } from "../../../src/MatrixClientPeg";
 import { NotificationLevel } from "../../../src/stores/notifications/NotificationLevel";
-
-jest.mock("../../../src/settings/SettingsStore");
+import { SettingLevel } from "../../../src/settings/SettingLevel";
+import MatrixClientBackedController from "../../../src/settings/controllers/MatrixClientBackedController";
+import SettingsStore from "../../../src/settings/SettingsStore";
 
 describe("notifications", () => {
     let accountDataStore: Record<string, MatrixEvent> = {};
@@ -44,6 +44,7 @@ describe("notifications", () => {
     beforeEach(() => {
         jest.clearAllMocks();
         mockClient = getMockClientWithEventEmitter({
+            ...mockClientMethodsServer(),
             isGuest: jest.fn().mockReturnValue(false),
             getAccountData: jest.fn().mockImplementation((eventType) => accountDataStore[eventType]),
             setAccountData: jest.fn().mockImplementation((eventType, content) => {
@@ -52,10 +53,20 @@ describe("notifications", () => {
                     content,
                 });
             }),
+            isVersionSupported: jest.fn().mockImplementation(async (v) => v === "v1.4"),
         });
+
+        // Ensure unstable settings are supported, otherwise it will use the default value.
+        MatrixClientBackedController.matrixClient = mockClient;
         accountDataStore = {};
         accountDataEventKey = getLocalNotificationAccountDataEventType(mockClient.deviceId!);
-        mocked(SettingsStore).getValue.mockReturnValue(false);
+        // Disable all notifications
+        deviceNotificationSettingsKeys.forEach((k) => SettingsStore.setValue(k, null, SettingLevel.DEVICE, false));
+    });
+
+    afterEach(() => {
+        jest.restoreAllMocks();
+        SettingsStore.reset();
     });
 
     describe("createLocalNotification", () => {
@@ -75,10 +86,15 @@ describe("notifications", () => {
         it.each(deviceNotificationSettingsKeys)(
             "unsilenced for existing sessions when %s setting is truthy",
             async (settingKey) => {
-                mocked(SettingsStore).getValue.mockImplementation((key): any => {
-                    return key === settingKey;
+                // We need to spy `getValue` because setting these keys requires mocking
+                // the platform to support notifications, which is out of scope for this test.
+                const origFn = SettingsStore.getValue;
+                jest.spyOn(SettingsStore, "getValue").mockImplementation((name, ...args) => {
+                    if (name === settingKey) {
+                        return true;
+                    }
+                    return origFn(name, ...args);
                 });
-
                 await createLocalNotificationSettingsIfNeeded(mockClient);
                 const event = mockClient.getAccountData(accountDataEventKey);
                 expect(event?.getContent().is_silenced).toBe(false);
@@ -116,7 +132,6 @@ describe("notifications", () => {
         const ROOM_ID = "123";
         const USER_ID = "@bob:example.org";
         let message: MatrixEvent;
-        let sendReceiptsSetting = true;
 
         beforeEach(() => {
             stubClient();
@@ -131,9 +146,7 @@ describe("notifications", () => {
             room.addLiveEvents([message], { addToState: true });
             sendReadReceiptSpy = jest.spyOn(client, "sendReadReceipt").mockResolvedValue({});
             jest.spyOn(client, "getRooms").mockReturnValue([room]);
-            jest.spyOn(SettingsStore, "getValue").mockImplementation((name) => {
-                return name === "sendReadReceipts" && sendReceiptsSetting;
-            });
+            SettingsStore.setValue("sendReadReceipts", null, SettingLevel.DEVICE, true);
         });
 
         it("sends a request even if everything has been read", async () => {
@@ -152,11 +165,8 @@ describe("notifications", () => {
         });
 
         describe("when sendReadReceipts setting is disabled", () => {
-            beforeEach(() => {
-                sendReceiptsSetting = false;
-            });
-
             it("should send a private read receipt", async () => {
+                SettingsStore.setValue("sendReadReceipts", null, SettingLevel.DEVICE, false);
                 await clearRoomNotification(room, client);
                 expect(sendReadReceiptSpy).toHaveBeenCalledWith(message, ReceiptType.ReadPrivate, true);
             });
@@ -177,9 +187,7 @@ describe("notifications", () => {
             room = new Room(ROOM_ID, client, USER_ID);
             sendReadReceiptSpy = jest.spyOn(client, "sendReadReceipt").mockResolvedValue({});
             jest.spyOn(client, "getRooms").mockReturnValue([room]);
-            jest.spyOn(SettingsStore, "getValue").mockImplementation((name) => {
-                return name === "sendReadReceipts";
-            });
+            SettingsStore.setValue("sendReadReceipts", null, SettingLevel.DEVICE, true);
         });
 
         it("does not send any requests if everything has been read", () => {
@@ -212,7 +220,7 @@ describe("notifications", () => {
             room.addLiveEvents([message], { addToState: true });
             room.setUnreadNotificationCount(NotificationCountType.Total, 1);
 
-            jest.spyOn(SettingsStore, "getValue").mockReset().mockReturnValue(false);
+            SettingsStore.setValue("sendReadReceipts", null, SettingLevel.DEVICE, false);
 
             await clearAllNotifications(client);