diff --git a/packages/edit-site/src/components/global-styles/variations/variation.js b/packages/edit-site/src/components/global-styles/variations/variation.js
index dc531b40635259..d2fa64ca64a27a 100644
--- a/packages/edit-site/src/components/global-styles/variations/variation.js
+++ b/packages/edit-site/src/components/global-styles/variations/variation.js
@@ -15,12 +15,19 @@ import { privateApis as blockEditorPrivateApis } from '@wordpress/block-editor';
  * Internal dependencies
  */
 import { mergeBaseAndUserConfigs } from '../global-styles-provider';
+import getValueFromObjectPath from '../../../utils/get-value-from-object-path';
+import setNestedValue from '../../../utils/set-nested-value';
 import { unlock } from '../../../lock-unlock';
 
 const { GlobalStylesContext, areGlobalStyleConfigsEqual } = unlock(
 	blockEditorPrivateApis
 );
 
+const PATHS_TO_AVOID_OVERWRITING = [
+	[ 'settings', 'typography', 'fontFamilies', 'custom' ],
+	[ 'settings', 'color', 'palette', 'custom' ],
+];
+
 export default function Variation( { variation, children } ) {
 	const [ isFocused, setIsFocused ] = useState( false );
 	const { base, user, setUserConfig } = useContext( GlobalStylesContext );
@@ -38,10 +45,20 @@ export default function Variation( { variation, children } ) {
 	);
 
 	const selectVariation = () => {
-		setUserConfig( () => ( {
-			settings: variation.settings,
-			styles: variation.styles,
-		} ) );
+		setUserConfig( ( currentConfig ) => {
+			// Avoids overwriting certain paths when applying a theme variation.
+			for ( const path of PATHS_TO_AVOID_OVERWRITING ) {
+				// Gets the value from the current config.
+				const value = getValueFromObjectPath( currentConfig, path );
+				// Sets the value in the applied variation.
+				setNestedValue( variation, path, value );
+			}
+
+			return {
+				settings: variation.settings,
+				styles: variation.styles,
+			};
+		} );
 	};
 
 	const selectOnEnter = ( event ) => {
diff --git a/packages/edit-site/src/hooks/push-changes-to-global-styles/index.js b/packages/edit-site/src/hooks/push-changes-to-global-styles/index.js
index 21f19201b75108..d6b0b5661546ae 100644
--- a/packages/edit-site/src/hooks/push-changes-to-global-styles/index.js
+++ b/packages/edit-site/src/hooks/push-changes-to-global-styles/index.js
@@ -27,6 +27,8 @@ import { store as coreStore } from '@wordpress/core-data';
 import { useSupportedStyles } from '../../components/global-styles/hooks';
 import { unlock } from '../../lock-unlock';
 import cloneDeep from '../../utils/clone-deep';
+import getValueFromObjectPath from '../../utils/get-value-from-object-path';
+import setNestedValue from '../../utils/set-nested-value';
 
 const { cleanEmptyObject, GlobalStylesContext } = unlock(
 	blockEditorPrivateApis
@@ -105,14 +107,6 @@ const STYLE_PATH_TO_PRESET_BLOCK_ATTRIBUTE = {
 
 const SUPPORTED_STYLES = [ 'border', 'color', 'spacing', 'typography' ];
 
-const getValueFromObjectPath = ( object, path ) => {
-	let value = object;
-	path.forEach( ( fieldName ) => {
-		value = value?.[ fieldName ];
-	} );
-	return value;
-};
-
 const flatBorderProperties = [ 'borderColor', 'borderWidth', 'borderStyle' ];
 const sides = [ 'top', 'right', 'bottom', 'left' ];
 
@@ -236,46 +230,6 @@ function useChangesToPush( name, attributes, userConfig ) {
 	}, [ supports, attributes, blockUserConfig ] );
 }
 
-/**
- * Sets the value at path of object.
- * If a portion of path doesn’t exist, it’s created.
- * Arrays are created for missing index properties while objects are created
- * for all other missing properties.
- *
- * This function intentionally mutates the input object.
- *
- * Inspired by _.set().
- *
- * @see https://lodash.com/docs/4.17.15#set
- *
- * @todo Needs to be deduplicated with its copy in `@wordpress/core-data`.
- *
- * @param {Object} object Object to modify
- * @param {Array}  path   Path of the property to set.
- * @param {*}      value  Value to set.
- */
-function setNestedValue( object, path, value ) {
-	if ( ! object || typeof object !== 'object' ) {
-		return object;
-	}
-
-	path.reduce( ( acc, key, idx ) => {
-		if ( acc[ key ] === undefined ) {
-			if ( Number.isInteger( path[ idx + 1 ] ) ) {
-				acc[ key ] = [];
-			} else {
-				acc[ key ] = {};
-			}
-		}
-		if ( idx === path.length - 1 ) {
-			acc[ key ] = value;
-		}
-		return acc[ key ];
-	}, object );
-
-	return object;
-}
-
 function PushChangesToGlobalStylesControl( {
 	name,
 	attributes,
diff --git a/packages/edit-site/src/utils/get-value-from-object-path.js b/packages/edit-site/src/utils/get-value-from-object-path.js
new file mode 100644
index 00000000000000..f1109904f24021
--- /dev/null
+++ b/packages/edit-site/src/utils/get-value-from-object-path.js
@@ -0,0 +1,7 @@
+export default function getValueFromObjectPath( object, path ) {
+	let value = object;
+	path.forEach( ( fieldName ) => {
+		value = value?.[ fieldName ];
+	} );
+	return value;
+}
diff --git a/packages/edit-site/src/utils/set-nested-value.js b/packages/edit-site/src/utils/set-nested-value.js
new file mode 100644
index 00000000000000..ec684e751cd041
--- /dev/null
+++ b/packages/edit-site/src/utils/set-nested-value.js
@@ -0,0 +1,39 @@
+/**
+ * Sets the value at path of object.
+ * If a portion of path doesn’t exist, it’s created.
+ * Arrays are created for missing index properties while objects are created
+ * for all other missing properties.
+ *
+ * This function intentionally mutates the input object.
+ *
+ * Inspired by _.set().
+ *
+ * @see https://lodash.com/docs/4.17.15#set
+ *
+ * @todo Needs to be deduplicated with its copy in `@wordpress/core-data`.
+ *
+ * @param {Object} object Object to modify
+ * @param {Array}  path   Path of the property to set.
+ * @param {*}      value  Value to set.
+ */
+export default function setNestedValue( object, path, value ) {
+	if ( ! object || typeof object !== 'object' ) {
+		return object;
+	}
+
+	path.reduce( ( acc, key, idx ) => {
+		if ( acc[ key ] === undefined ) {
+			if ( Number.isInteger( path[ idx + 1 ] ) ) {
+				acc[ key ] = [];
+			} else {
+				acc[ key ] = {};
+			}
+		}
+		if ( idx === path.length - 1 ) {
+			acc[ key ] = value;
+		}
+		return acc[ key ];
+	}, object );
+
+	return object;
+}