diff --git a/core/src/global/ionic-global.ts b/core/src/global/ionic-global.ts
index 2a4b49a93a7..e3ce11b1f4e 100644
--- a/core/src/global/ionic-global.ts
+++ b/core/src/global/ionic-global.ts
@@ -177,28 +177,38 @@ export const initialize = (userConfig: IonicConfig = {}) => {
   }
 
   /**
-   * Apply any global config values from the custom theme
-   * excluding component-specific overrides.
+   * Apply any global config values from the resolved theme
+   * excluding component-specific overrides. The resolved theme
+   * is the base theme merged with the custom theme, so a value
+   * from the custom theme takes precedence over the base theme.
+   * The theme only provides defaults, so any value set by the
+   * application takes precedence over the value from the theme.
    */
+  const resolvedTheme: DefaultTheme | undefined = config.get('customTheme');
   // eslint-disable-next-line @typescript-eslint/no-unused-vars
-  const { components, ...customGlobalConfig } = customTheme?.config || {};
+  const { components, ...themeGlobalConfig } = resolvedTheme?.config || {};
 
-  Object.entries(customGlobalConfig).forEach(([key, value]) => {
+  const isPlainObject = (value: unknown): value is Record<string, unknown> =>
+    typeof value === 'object' && value !== null && !Array.isArray(value);
+
+  Object.entries(themeGlobalConfig).forEach(([key, value]) => {
     const configKey = key as keyof IonicConfig;
+    const appValue = config.get(configKey);
 
-    // For object-based config values, we merge with existing settings.
-    if (value !== null && typeof value === 'object') {
-      const existingConfig = config.get(configKey, {});
-      config.set(configKey, { ...existingConfig, ...value });
+    // The theme value is used when the application has not set one.
+    if (appValue === undefined) {
+      config.set(configKey, value);
       return;
     }
 
     /**
-     * For primitive values (boolean, string, number), we set the
-     * value directly.
-     * This covers global flags like 'rippleEffect' or 'animated'.
+     * For object-based config values, such as 'screenBreakpoints',
+     * the theme fills in the keys the application has not set.
+     * Any other value set by the application is kept as is.
      */
-    config.set(configKey, value);
+    if (isPlainObject(value) && isPlainObject(appValue)) {
+      config.set(configKey, { ...value, ...appValue });
+    }
   });
 
   /**
diff --git a/core/src/global/test/ionic-global.spec.ts b/core/src/global/test/ionic-global.spec.ts
index 25f431de538..1fce165aa06 100644
--- a/core/src/global/test/ionic-global.spec.ts
+++ b/core/src/global/test/ionic-global.spec.ts
@@ -138,9 +138,9 @@ describe('Ionic Global', () => {
     });
 
     /**
-     * A theme can set the screen breakpoints in its own config block, which is
-     * merged in after the application config, so the listeners can only be
-     * rebuilt once both have been applied.
+     * A theme can set the screen breakpoints in its own config block, which
+     * provides defaults for the application config, so the listeners can only
+     * be rebuilt once both have been applied.
      */
     it('should rebuild the breakpoint listeners from a theme that sets the widths', () => {
       // Subscribing first is what creates the listeners there are to rebuild.
@@ -156,8 +156,8 @@ describe('Ionic Global', () => {
     });
 
     /**
-     * The theme's config is merged over the application's, so widths set in
-     * either are kept and the listeners are built from the result.
+     * The theme's config fills in the widths the application has not set, so
+     * widths set in either are kept and the listeners are built from the result.
      */
     it('should keep widths set by the application alongside those from the theme', () => {
       const unsubscribe = onBreakpointChange(() => {});
@@ -174,6 +174,69 @@ describe('Ionic Global', () => {
       unsubscribe();
     });
 
+    it('should use the application value over the theme value for a primitive config option', () => {
+      initialize({
+        rippleEffect: false,
+        formHighlight: false,
+        customTheme: { config: { rippleEffect: true, formHighlight: true } },
+      } as any);
+
+      expect(config.get('rippleEffect')).toBe(false);
+      expect(config.get('formHighlight')).toBe(false);
+    });
+
+    it('should use the theme value for a config option the application has not set', () => {
+      initialize({ customTheme: { config: { rippleEffect: true } } } as any);
+
+      expect(config.get('rippleEffect')).toBe(true);
+    });
+
+    it('should use the application value over the theme value for an overlapping object key', () => {
+      initialize({
+        screenBreakpoints: { md: 500, lg: 900 },
+        customTheme: { config: { screenBreakpoints: { md: 700, xl: 1300 } } },
+      } as any);
+
+      expect(config.get('screenBreakpoints')).toEqual({ md: 500, lg: 900, xl: 1300 });
+    });
+
+    it('should keep an application value that is not an object when the theme value is', () => {
+      initialize({
+        screenBreakpoints: 'invalid',
+        customTheme: { config: { screenBreakpoints: { md: 700 } } },
+      } as any);
+
+      expect(config.get('screenBreakpoints')).toBe('invalid');
+    });
+
+    it('should apply the base theme config when no custom theme is provided', () => {
+      initialize();
+
+      expect(config.get('formHighlight')).toBe(false);
+    });
+
+    it('should use the custom theme value over the base theme value', () => {
+      initialize({ customTheme: { config: { formHighlight: true } } } as any);
+
+      expect(config.get('formHighlight')).toBe(true);
+    });
+
+    it('should use the application value over the base theme value', () => {
+      initialize({ formHighlight: true } as any);
+
+      expect(config.get('formHighlight')).toBe(true);
+    });
+
+    /**
+     * Ripple effects are enabled by default for the md theme through the
+     * tap-click fallback, so the base theme must leave the value unset.
+     */
+    it('should not set the ripple effect when no custom theme is provided', () => {
+      initialize();
+
+      expect(config.get('rippleEffect')).toBeUndefined();
+    });
+
     /**
      * The media queries are generated from the configured widths too, so they
      * have to be emitted once the theme's config has been merged as well.
diff --git a/core/src/themes/base/default.tokens.ts b/core/src/themes/base/default.tokens.ts
index 26906072d12..f9b6d8817be 100644
--- a/core/src/themes/base/default.tokens.ts
+++ b/core/src/themes/base/default.tokens.ts
@@ -17,7 +17,6 @@ export const defaultTheme: DefaultTheme = {
 
   config: {
     formHighlight: false,
-    rippleEffect: false,
   },
 
   spacing: {