diff --git a/package.json b/package.json
index 4dda7d51248e..d964835cf104 100644
--- a/package.json
+++ b/package.json
@@ -50,7 +50,7 @@
     "check-dependencies": "node ./scripts/check-mismatched-dependencies.cjs",
     "docs": "run-s docs:build docs:update-functions-path",
     "docs:build": "typedoc --tsconfig tsconfig.build.json",
-    "docs:markdown-for-agoric-documentation-repo": "run-s docs:markdown-build docs:update-functions-path",
+    "docs:markdown-for-agoric-documentation-repo": "run-s docs:markdown-build 'docs:update-functions-path md'",
     "docs:markdown-build": "typedoc --plugin typedoc-plugin-markdown --tsconfig tsconfig.build.json",
     "docs:update-functions-path": "node ./scripts/update-typedoc-functions-path.cjs",
     "lerna": "lerna",
diff --git a/scripts/update-typedoc-functions-path.cjs b/scripts/update-typedoc-functions-path.cjs
index 7804889a0e82..734df479437f 100644
--- a/scripts/update-typedoc-functions-path.cjs
+++ b/scripts/update-typedoc-functions-path.cjs
@@ -11,6 +11,9 @@
  * 2. updates generated urls in html files to reference new url path
  * 3. updates base64 encoded navigation state to reference new url path
  *
+ * If an `md` argument is supplied - versus the optional default `html` document -
+ * a different set of logic will run to update paths are links for markdown files.
+ *
  * See https://github.com/TypeStrong/typedoc/issues/2111 for more solutions
  * on how to workaround this.
  *
@@ -22,15 +25,20 @@
 const fsp = require('fs').promises;
 const path = require('path');
 const zlib = require('zlib');
-
-const navigationFilePath = path.join(
-  __dirname,
-  '..',
-  'api-docs',
-  'assets',
-  'navigation.js',
-);
-const apiDocsDir = path.join(__dirname, '..', 'api-docs');
+const process = require('process');
+
+const config = {
+  oldDirName: 'functions',
+  newDirName: 'funcs',
+  apiDocsDir: path.join(__dirname, '..', 'api-docs'),
+  navigationFilePath: path.join(
+    __dirname,
+    '..',
+    'api-docs',
+    'assets',
+    'navigation.js',
+  ),
+};
 
 // Decodes and decompresses the TypeDoc navigation data
 function decodeTypeDocNavigation(encodedData) {
@@ -94,64 +102,109 @@ function updateUrls(data, searchString, replaceString) {
   return data;
 }
 
-// Updates href links in HTML files
-async function updateHtmlFiles(dir, searchString, replaceString) {
+// Updates js-based navigation state
+async function updateNavigationFile() {
+  const fileContent = await fsp.readFile(config.navigationFilePath, 'utf8');
+  const match = fileContent.match(/window\.navigationData = "(.*?)"/);
+  if (!match) {
+    throw new Error('Navigation data not found in file');
+  }
+  const encodedData = match[1];
+
+  const decodedData = await decodeTypeDocNavigation(encodedData);
+  const updatedData = updateUrls(
+    decodedData,
+    config.oldDirName,
+    config.newDirName,
+  );
+  const newEncodedData = await encodeTypeDocNavigation(updatedData);
+  const newFileContent = `window.navigationData = "${newEncodedData}"`;
+  await fsp.writeFile(config.navigationFilePath, newFileContent);
+  console.log('Navigation file updated successfully');
+}
+
+/**
+ * Updates files in a directory
+ * @param {string} dir - Directory to update
+ * @param {string} fileExtension - File extension to process
+ * @param {Function} updateFunction - Function to update file content
+ */
+async function updateFiles(dir, fileExtension, updateFunction) {
   const files = await fsp.readdir(dir);
   for (const file of files) {
     const filePath = path.join(dir, file);
     const stat = await fsp.stat(filePath);
     if (stat.isDirectory()) {
-      await updateHtmlFiles(filePath, searchString, replaceString);
-    } else if (path.extname(file) === '.html') {
-      let content = await fsp.readFile(filePath, 'utf8');
-      if (content.includes(`/${searchString}/`)) {
-        content = content.replace(
-          new RegExp(`/${searchString}/`, 'g'),
-          `/${replaceString}/`,
-        );
-        await fsp.writeFile(filePath, content);
+      if (file === config.oldDirName) {
+        const newPath = path.join(dir, config.newDirName);
+        await fsp.rename(filePath, newPath);
+        console.log(`Renamed directory: ${filePath} to ${newPath}`);
+        await updateFiles(newPath, fileExtension, updateFunction);
+      } else {
+        await updateFiles(filePath, fileExtension, updateFunction);
+      }
+    } else if (path.extname(file) === fileExtension) {
+      const content = await fsp.readFile(filePath, 'utf8');
+      const updatedContent = updateFunction(content);
+      if (content !== updatedContent) {
+        await fsp.writeFile(filePath, updatedContent);
         console.log(`Updated: ${filePath}`);
       }
     }
   }
 }
 
-// Updates the navigation file and HTML files in the api-docs directory
-// replacing /function file names and url references with /funcs
-async function updateNavigationAndHtmlFiles(
-  searchString = 'functions',
-  replaceString = 'funcs',
-) {
-  await null;
-  try {
-    // Rename the directory
-    const oldDirPath = path.join(apiDocsDir, searchString);
-    const newDirPath = path.join(apiDocsDir, replaceString);
-    await fsp.rename(oldDirPath, newDirPath);
-    console.log(`Directory renamed from ${searchString} to ${replaceString}`);
-
-    // Update navigation file
-    const fileContent = await fsp.readFile(navigationFilePath, 'utf8');
-    const match = fileContent.match(/window\.navigationData = "(.*?)"/);
-    if (!match) {
-      throw new Error('Navigation data not found in file');
-    }
-    const encodedData = match[1];
-
-    const decodedData = await decodeTypeDocNavigation(encodedData);
-    const updatedData = updateUrls(decodedData, searchString, replaceString);
-    const newEncodedData = await encodeTypeDocNavigation(updatedData);
-    const newFileContent = `window.navigationData = "${newEncodedData}"`;
-    await fsp.writeFile(navigationFilePath, newFileContent);
+/**
+ * Updates content in Markdown files
+ * @param {string} content - The Markdown content to update
+ * @returns {string} - The updated Markdown content
+ */
+function updateMarkdownContentLinks(content) {
+  return (
+    content
+      // Update links like [text](functions/file.md)
+      .replace(
+        new RegExp(`\\[(.*?)\\]\\(${config.oldDirName}/`, 'g'),
+        `[$1](${config.newDirName}/`,
+      )
+      // Update links like [text](../functions/file.md)
+      .replace(
+        new RegExp(`\\[(.*?)\\]\\(\\.\\./${config.oldDirName}/`, 'g'),
+        `[$1](../${config.newDirName}/`,
+      )
+  );
+}
 
-    console.log('Navigation file updated successfully');
+/**
+ * Updates content in HTML files
+ * @param {string} content - The HTML content to update
+ * @returns {string} - The updated HTML content
+ */
+function updateHtmlContentLinks(content) {
+  return content.replace(
+    new RegExp(`/${config.oldDirName}/`, 'g'),
+    `/${config.newDirName}/`,
+  );
+}
 
-    // Update HTML files
-    await updateHtmlFiles(apiDocsDir, searchString, replaceString);
-    console.log('HTML files updated successfully');
-  } catch (error) {
-    console.error('Error updating files:', error);
+/**
+ * Main function to run the script
+ */
+async function main() {
+  const fileType = process.argv[2] || 'html';
+  await null;
+  switch (fileType) {
+    case 'html':
+      await updateFiles(config.apiDocsDir, '.html', updateHtmlContentLinks);
+      return updateNavigationFile();
+    case 'md':
+      return updateFiles(config.apiDocsDir, '.md', updateMarkdownContentLinks);
+    default:
+      throw new Error('Invalid file type. Use "html" or "md".');
   }
 }
 
-updateNavigationAndHtmlFiles().catch(e => console.error(e));
+main().catch(e => {
+  console.error(`Error: ${e.message}`);
+  process.exit(1);
+});