diff --git a/docs/config/setup/interfaces/mermaid.Mermaid.md b/docs/config/setup/interfaces/mermaid.Mermaid.md
index 86bdbe8fa..c139125f9 100644
--- a/docs/config/setup/interfaces/mermaid.Mermaid.md
+++ b/docs/config/setup/interfaces/mermaid.Mermaid.md
@@ -165,7 +165,7 @@ Internal helpers for mermaid
 
 ### mermaidAPI
 
-• **mermaidAPI**: `Readonly`<{ `defaultConfig`: [`MermaidConfig`](mermaid.MermaidConfig.md) = configApi.defaultConfig; `getConfig`: () => [`MermaidConfig`](mermaid.MermaidConfig.md) = configApi.getConfig; `getDiagramFromText`: (`text`: `string`, `metadata`: `Pick`<`DiagramMetadata`, `"title"`>) => `Promise`<`Diagram`> ; `getSiteConfig`: () => [`MermaidConfig`](mermaid.MermaidConfig.md) = configApi.getSiteConfig; `globalReset`: () => `void` ; `initialize`: (`options`: [`MermaidConfig`](mermaid.MermaidConfig.md)) => `void` ; `parse`: (`text`: `string`, `parseOptions`: [`ParseOptions`](mermaid.ParseOptions.md) & { `suppressErrors`: `true` }) => `Promise`<[`ParseResult`](mermaid.ParseResult.md) | `false`>(`text`: `string`, `parseOptions?`: [`ParseOptions`](mermaid.ParseOptions.md)) => `Promise`<[`ParseResult`](mermaid.ParseResult.md)> ; `render`: (`id`: `string`, `text`: `string`, `svgContainingElement?`: `Element`) => `Promise`<[`RenderResult`](mermaid.RenderResult.md)> ; `reset`: () => `void` ; `setConfig`: (`conf`: [`MermaidConfig`](mermaid.MermaidConfig.md)) => [`MermaidConfig`](mermaid.MermaidConfig.md) = configApi.setConfig; `updateSiteConfig`: (`conf`: [`MermaidConfig`](mermaid.MermaidConfig.md)) => [`MermaidConfig`](mermaid.MermaidConfig.md) = configApi.updateSiteConfig }>
+• **mermaidAPI**: `Readonly`<{ `defaultConfig`: [`MermaidConfig`](mermaid.MermaidConfig.md) = configApi.defaultConfig; `getConfig`: () => [`MermaidConfig`](mermaid.MermaidConfig.md) = configApi.getConfig; `getDiagramFromText`: (`text`: `string`, `metadata`: `Pick`<`DiagramMetadata`, `"title"`>) => `Promise`<`Diagram`> ; `getSiteConfig`: () => [`MermaidConfig`](mermaid.MermaidConfig.md) = configApi.getSiteConfig; `globalReset`: () => `void` ; `initialize`: (`userOptions`: [`MermaidConfig`](mermaid.MermaidConfig.md)) => `void` ; `parse`: (`text`: `string`, `parseOptions`: [`ParseOptions`](mermaid.ParseOptions.md) & { `suppressErrors`: `true` }) => `Promise`<[`ParseResult`](mermaid.ParseResult.md) | `false`>(`text`: `string`, `parseOptions?`: [`ParseOptions`](mermaid.ParseOptions.md)) => `Promise`<[`ParseResult`](mermaid.ParseResult.md)> ; `render`: (`id`: `string`, `text`: `string`, `svgContainingElement?`: `Element`) => `Promise`<[`RenderResult`](mermaid.RenderResult.md)> ; `reset`: () => `void` ; `setConfig`: (`conf`: [`MermaidConfig`](mermaid.MermaidConfig.md)) => [`MermaidConfig`](mermaid.MermaidConfig.md) = configApi.setConfig; `updateSiteConfig`: (`conf`: [`MermaidConfig`](mermaid.MermaidConfig.md)) => [`MermaidConfig`](mermaid.MermaidConfig.md) = configApi.updateSiteConfig }>
 
 **`Deprecated`**
 
diff --git a/packages/mermaid/src/mermaidAPI.ts b/packages/mermaid/src/mermaidAPI.ts
index e336f1036..e1c4412b9 100644
--- a/packages/mermaid/src/mermaidAPI.ts
+++ b/packages/mermaid/src/mermaidAPI.ts
@@ -25,6 +25,7 @@ import { preprocessDiagram } from './preprocess.js';
 import { decodeEntities } from './utils.js';
 import { toBase64 } from './utils/base64.js';
 import type { D3Element, ParseOptions, ParseResult, RenderResult } from './types.js';
+import assignWithDepth from './assignWithDepth.js';
 
 const MAX_TEXTLENGTH = 50_000;
 const MAX_TEXTLENGTH_EXCEEDED_MSG =
@@ -473,9 +474,10 @@ const render = async function (
 };
 
 /**
- * @param  options - Initial Mermaid options
+ * @param  userOptions - Initial Mermaid options
  */
-function initialize(options: MermaidConfig = {}) {
+function initialize(userOptions: MermaidConfig = {}) {
+  const options = assignWithDepth({}, userOptions);
   // Handle legacy location of font-family configuration
   if (options?.fontFamily && !options.themeVariables?.fontFamily) {
     if (!options.themeVariables) {