diff --git a/res/css/_common.pcss b/res/css/_common.pcss
index 855c64cb73..1ab0e8bf5d 100644
--- a/res/css/_common.pcss
+++ b/res/css/_common.pcss
@@ -17,7 +17,7 @@ See the License for the specific language governing permissions and
 limitations under the License.
 */
 
-@import url("@vector-im/compound-design-tokens/assets/web/css/compound-design-tokens.css");
+@import url("@vector-im/compound-design-tokens/assets/web/css/compound-design-tokens.css") layer(compound);
 @import url("@vector-im/compound-web/dist/style.css");
 @import "./_font-sizes.pcss";
 @import "./_animations.pcss";
diff --git a/res/css/views/rooms/_JumpToBottomButton.pcss b/res/css/views/rooms/_JumpToBottomButton.pcss
index 08e3ad9031..0a760e2cd6 100644
--- a/res/css/views/rooms/_JumpToBottomButton.pcss
+++ b/res/css/views/rooms/_JumpToBottomButton.pcss
@@ -14,8 +14,6 @@ See the License for the specific language governing permissions and
 limitations under the License.
 */
 
-@charset "utf-8";
-
 .mx_JumpToBottomButton {
     z-index: 1000;
     position: absolute;
diff --git a/res/css/views/rooms/_TopUnreadMessagesBar.pcss b/res/css/views/rooms/_TopUnreadMessagesBar.pcss
index 258adb759a..e72fedafef 100644
--- a/res/css/views/rooms/_TopUnreadMessagesBar.pcss
+++ b/res/css/views/rooms/_TopUnreadMessagesBar.pcss
@@ -14,8 +14,6 @@ See the License for the specific language governing permissions and
 limitations under the License.
 */
 
-@charset "utf-8";
-
 .mx_TopUnreadMessagesBar {
     z-index: 1000;
     position: absolute;
diff --git a/res/themes/light-custom/css/_custom.pcss b/res/themes/light-custom/css/_custom.pcss
index 5ecac33ffc..ed345a28ec 100644
--- a/res/themes/light-custom/css/_custom.pcss
+++ b/res/themes/light-custom/css/_custom.pcss
@@ -32,9 +32,6 @@ $background: var(--background, $background);
 $panels: var(--panels, var(--cpd-color-gray-600));
 $panel-actions: var(--panels-actions, var(--cpd-color-gray-300));
 
-/* --accent-color */
-$username-variant3-color: var(--accent-color);
-
 /* --timeline-background-color */
 $button-secondary-bg-color: var(--timeline-background-color);
 $lightbox-border-color: var(--timeline-background-color);
@@ -110,14 +107,6 @@ $accent-alt: var(--primary-color);
 /* --warning-color */
 $button-danger-disabled-bg-color: var(--warning-color-50pct); /* still needs alpha at 0.5 */
 
-/* --username colors (which use a 0-based index) */
-$username-variant1-color: var(--username-colors_0, $username-variant1-color);
-$username-variant2-color: var(--username-colors_1, $username-variant2-color);
-$username-variant3-color: var(--username-colors_2, $username-variant3-color);
-$username-variant4-color: var(--username-colors_3, $username-variant4-color);
-$username-variant5-color: var(--username-colors_4, $username-variant5-color);
-$username-variant6-color: var(--username-colors_5, $username-variant6-color);
-
 /* --timeline-highlights-color */
 $event-selected-color: var(--timeline-highlights-color);
 $event-highlight-bg-color: var(--timeline-highlights-color);
diff --git a/res/themes/light/css/light.pcss b/res/themes/light/css/light.pcss
index 612e8fdce6..361484828f 100644
--- a/res/themes/light/css/light.pcss
+++ b/res/themes/light/css/light.pcss
@@ -1,5 +1,3 @@
-@import url("@vector-im/compound-design-tokens/assets/web/css/compound-design-tokens.css");
-
 @import "../../../../res/css/_font-sizes.pcss";
 @import "_paths.pcss";
 @import "_fonts.pcss";
diff --git a/src/theme.ts b/src/theme.ts
index 1d5376b6c1..8e2e893334 100644
--- a/src/theme.ts
+++ b/src/theme.ts
@@ -35,17 +35,22 @@ interface IFontFaces extends Omit<Record<(typeof allowedFontFaceProps)[number],
     }[];
 }
 
+interface CompoundTheme {
+    [token: string]: string;
+}
+
 export type CustomTheme = {
     name: string;
-    colors: {
+    is_dark?: boolean; // eslint-disable-line camelcase
+    colors?: {
         [key: string]: string;
     };
-    fonts: {
+    fonts?: {
         faces: IFontFaces[];
         general: string;
         monospace: string;
     };
-    is_dark?: boolean; // eslint-disable-line camelcase
+    compound?: CompoundTheme;
 };
 
 /**
@@ -120,10 +125,10 @@ function clearCustomTheme(): void {
             document.body.style.removeProperty(prop);
         }
     }
-    const customFontFaceStyle = document.querySelector("head > style[title='custom-theme-font-faces']");
-    if (customFontFaceStyle) {
-        customFontFaceStyle.remove();
-    }
+
+    // remove the custom style sheets
+    document.querySelector("head > style[title='custom-theme-font-faces']")?.remove();
+    document.querySelector("head > style[title='custom-theme-compound']")?.remove();
 }
 
 const allowedFontFaceProps = [
@@ -177,6 +182,22 @@ function generateCustomFontFaceCSS(faces: IFontFaces[]): string {
         .join("\n");
 }
 
+const COMPOUND_TOKEN = /^--cpd-[a-z0-9-]+$/;
+
+/**
+ * Generates a style sheet to override Compound design tokens as specified in
+ * the given theme.
+ */
+function generateCustomCompoundCSS(theme: CompoundTheme): string {
+    const properties: string[] = [];
+    for (const [token, value] of Object.entries(theme))
+        if (COMPOUND_TOKEN.test(token)) properties.push(`${token}: ${value};`);
+        else logger.warn(`'${token}' is not a valid Compound token`);
+    // Insert the design token overrides into the 'custom' cascade layer as
+    // documented at https://compound.element.io/?path=/docs/develop-theming--docs
+    return `@layer compound.custom { :root, [class*="cpd-theme-"] { ${properties.join(" ")} } }`;
+}
+
 function setCustomThemeVars(customTheme: CustomTheme): void {
     const { style } = document.body;
 
@@ -218,6 +239,14 @@ function setCustomThemeVars(customTheme: CustomTheme): void {
             style.setProperty("--font-family-monospace", fonts.monospace);
         }
     }
+    if (customTheme.compound) {
+        const css = generateCustomCompoundCSS(customTheme.compound);
+        const style = document.createElement("style");
+        style.setAttribute("title", "custom-theme-compound");
+        style.setAttribute("type", "text/css");
+        style.appendChild(document.createTextNode(css));
+        document.head.appendChild(style);
+    }
 }
 
 export function getCustomTheme(themeName: string): CustomTheme {
@@ -284,9 +313,6 @@ export async function setTheme(theme?: string): Promise<void> {
      * Adds the Compound theme class to the top-most element in the document
      * This will automatically refresh the colour scales based on the OS or user
      * preferences
-     *
-     * Note: Theming through Compound is not yet established. Brand theming should
-     * be done in a similar manner as it used to be done.
      */
     document.body.classList.remove("cpd-theme-light", "cpd-theme-dark", "cpd-theme-light-hc", "cpd-theme-dark-hc");
 
diff --git a/test/__snapshots__/theme-test.ts.snap b/test/__snapshots__/theme-test.ts.snap
new file mode 100644
index 0000000000..754786eb70
--- /dev/null
+++ b/test/__snapshots__/theme-test.ts.snap
@@ -0,0 +1,3 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`theme setTheme applies a custom Compound theme 1`] = `"@layer compound.custom { :root, [class*="cpd-theme-"] { --cpd-color-icon-accent-tertiary: var(--cpd-color-blue-800); --cpd-color-text-action-accent: var(--cpd-color-blue-900); } }"`;
diff --git a/test/theme-test.ts b/test/theme-test.ts
index 3789028f81..fdba6d0d18 100644
--- a/test/theme-test.ts
+++ b/test/theme-test.ts
@@ -21,31 +21,26 @@ describe("theme", () => {
     describe("setTheme", () => {
         let lightTheme: HTMLStyleElement;
         let darkTheme: HTMLStyleElement;
+        let lightCustomTheme: HTMLStyleElement;
 
         let spyQuerySelectorAll: jest.MockInstance<NodeListOf<Element>, [selectors: string]>;
         let spyClassList: jest.SpyInstance<void, string[], any>;
 
         beforeEach(() => {
-            const styles = [
-                {
-                    dataset: {
-                        mxTheme: "light",
-                    },
-                    disabled: true,
-                    href: "urlLight",
-                    onload: (): void => void 0,
-                } as unknown as HTMLStyleElement,
-                {
-                    dataset: {
-                        mxTheme: "dark",
-                    },
-                    disabled: true,
-                    href: "urlDark",
-                    onload: (): void => void 0,
-                } as unknown as HTMLStyleElement,
-            ];
+            const styles = ["light", "dark", "light-custom", "dark-custom"].map(
+                (theme) =>
+                    ({
+                        dataset: {
+                            mxTheme: theme,
+                        },
+                        disabled: true,
+                        href: "fake URL",
+                        onload: (): void => void 0,
+                    }) as unknown as HTMLStyleElement,
+            );
             lightTheme = styles[0];
             darkTheme = styles[1];
+            lightCustomTheme = styles[2];
 
             jest.spyOn(document.body, "style", "get").mockReturnValue([] as any);
             spyQuerySelectorAll = jest.spyOn(document, "querySelectorAll").mockReturnValue(styles as any);
@@ -124,6 +119,27 @@ describe("theme", () => {
                 jest.advanceTimersByTime(200 * 10);
             });
         });
+
+        it("applies a custom Compound theme", async () => {
+            jest.spyOn(SettingsStore, "getValue").mockReturnValue([
+                {
+                    name: "blue",
+                    compound: {
+                        "--cpd-color-icon-accent-tertiary": "var(--cpd-color-blue-800)",
+                        "--cpd-color-text-action-accent": "var(--cpd-color-blue-900)",
+                    },
+                },
+            ]);
+
+            const spy = jest.spyOn(document.head, "appendChild").mockImplementation();
+            await new Promise((resolve) => {
+                setTheme("custom-blue").then(resolve);
+                lightCustomTheme.onload!({} as Event);
+            });
+            expect(spy).toHaveBeenCalled();
+            expect(spy.mock.calls[0][0].textContent).toMatchSnapshot();
+            spy.mockRestore();
+        });
     });
 
     describe("enumerateThemes", () => {
diff --git a/yarn.lock b/yarn.lock
index 3c5af658a7..a7760b3f5d 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -3123,9 +3123,9 @@
   integrity sha512-zuVdFrMJiuCDQUMCzQaD6KL28MjnqqN8XnAqiEq9PNm/hCPTSGfrXCOfwj1ow4LFb/tNymJPwsNbVePc1xFqrQ==
 
 "@vector-im/compound-design-tokens@^1.0.0":
-  version "1.0.0"
-  resolved "https://registry.yarnpkg.com/@vector-im/compound-design-tokens/-/compound-design-tokens-1.0.0.tgz#4fe7744bbe0bd093b064d42ca8bb475862bb2ce7"
-  integrity sha512-/hKAxE/WsmnNZamlSmLoFeAhNDhRpFdJYuY8NrPLaS/dKS/QRnty6UYzs9yWOVNFeiBfkNsrb7wYIFMrYWSRJw==
+  version "1.1.0"
+  resolved "https://registry.yarnpkg.com/@vector-im/compound-design-tokens/-/compound-design-tokens-1.1.0.tgz#9b1a91317c404a1cd0d76d2fd5a7f2df5f1bf0a6"
+  integrity sha512-1HcCm6YsOda98rGXO4fg0WjEdrMnx/0tdtFmYIlnYkDYTbnfpFg+ffIDY7jgammWbOYwUZpZhM5q9ofb7/EgkA==
   dependencies:
     svg2vectordrawable "^2.9.1"