diff --git a/src/__tests__/formatting-run.test.ts b/src/__tests__/formatting-run.test.ts
index 21d87c2..bd89042 100644
--- a/src/__tests__/formatting-run.test.ts
+++ b/src/__tests__/formatting-run.test.ts
@@ -55,6 +55,39 @@ describe("formatMarkdownDocument", () => {
         )
     })
 
+    it("formats GitHub URLs in frontmatter without moving body-only formatting into frontmatter", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "notes/TypeScript" }],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const result = formatMarkdownDocument({
+            content:
+                "---\nautomatic-linker-disable-url-title: true\nreference: https://github.com/openai/openai/issues/1\nterm: TypeScript\n---\nTypeScript https://example.com",
+            filePath: "current-file.md",
+            frontmatter: {
+                "automatic-linker-disable-url-title": true,
+            },
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: true,
+                formatJiraURLs: false,
+                formatLinearURLs: false,
+                replaceUrlWithTitle: true,
+                ignoreCase: true,
+            },
+            candidateIndex: { candidateMap, trie },
+        })
+
+        expect(result).toBe(
+            "---\nautomatic-linker-disable-url-title: true\nreference: [[github/openai/openai/issues/1]] [🔗](https://github.com/openai/openai/issues/1)\nterm: TypeScript\n---\n[[notes/TypeScript|TypeScript]] https://example.com",
+        )
+    })
+
     it("runs URL formatting, URL titles, and link replacement in order", () => {
         const { candidateMap, trie } = buildCandidateTrieForTest({
             files: [{ path: "notes/TypeScript" }],
diff --git a/src/formatting-run.ts b/src/formatting-run.ts
index a3e9320..1b1a040 100644
--- a/src/formatting-run.ts
+++ b/src/formatting-run.ts
@@ -44,6 +44,25 @@ export const toReplaceLinksSettings = (
     ignoreMarkdownTables: settings.ignoreMarkdownTables,
 })
 
+const formatMarkdownURLs = (
+    text: string,
+    settings: AutomaticLinkerSettings,
+): string => {
+    let updatedText = text
+
+    if (settings.formatGitHubURLs) {
+        updatedText = replaceURLs(updatedText, settings, formatGitHubURL)
+    }
+    if (settings.formatJiraURLs) {
+        updatedText = replaceURLs(updatedText, settings, formatJiraURL)
+    }
+    if (settings.formatLinearURLs) {
+        updatedText = replaceURLs(updatedText, settings, formatLinearURL)
+    }
+
+    return updatedText
+}
+
 export const formatMarkdownBody = ({
     body,
     filePath,
@@ -54,17 +73,8 @@ export const formatMarkdownBody = ({
     urlTitleMap = new Map(),
     linkGenerator,
 }: Omit<FormattingRunOptions, "content"> & { body: string }): string => {
-    let updatedBody = body
+    let updatedBody = formatMarkdownURLs(body, settings)
 
-    if (settings.formatGitHubURLs) {
-        updatedBody = replaceURLs(updatedBody, settings, formatGitHubURL)
-    }
-    if (settings.formatJiraURLs) {
-        updatedBody = replaceURLs(updatedBody, settings, formatJiraURL)
-    }
-    if (settings.formatLinearURLs) {
-        updatedBody = replaceURLs(updatedBody, settings, formatLinearURL)
-    }
     if (settings.replaceUrlWithTitle && !isUrlTitleReplacementOff(frontmatter)) {
         updatedBody = replaceUrlWithTitle({ body: updatedBody, urlTitleMap })
     }
@@ -118,7 +128,10 @@ export const formatMarkdownDocument = ({
     contentStart = inferContentStart(content),
     ...options
 }: FormattingRunOptions): string => {
-    const frontmatterText = content.slice(0, contentStart)
+    const frontmatterText = formatMarkdownURLs(
+        content.slice(0, contentStart),
+        options.settings,
+    )
     const body = content.slice(contentStart)
     return frontmatterText + formatMarkdownBody({ ...options, body })
 }