diff --git a/src/__tests__/formatting-run.test.ts b/src/__tests__/formatting-run.test.ts
index bd89042..ed43131 100644
--- a/src/__tests__/formatting-run.test.ts
+++ b/src/__tests__/formatting-run.test.ts
@@ -175,4 +175,34 @@ describe("formatMarkdownSelection", () => {
             "[[notes/TypeScript|TypeScript]] https://github.com/openai/openai/issues/1",
         )
     })
+
+    it("leaves linear URLs unchanged when a linear note exists", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "notes/linear" },
+                { path: "notes/TypeScript" },
+            ],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const result = formatMarkdownSelection({
+            body: "linear://workspace/issue/ACME-123",
+            filePath: "current-file.md",
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: true,
+                formatJiraURLs: true,
+                formatLinearURLs: true,
+                replaceUrlWithTitle: true,
+                ignoreCase: true,
+            },
+            candidateIndex: { candidateMap, trie },
+        })
+
+        expect(result).toBe("linear://workspace/issue/ACME-123")
+    })
 })
diff --git a/src/__tests__/markdown-segments.test.ts b/src/__tests__/markdown-segments.test.ts
index f64f4a0..2a16760 100644
--- a/src/__tests__/markdown-segments.test.ts
+++ b/src/__tests__/markdown-segments.test.ts
@@ -62,6 +62,23 @@ describe("segmentMarkdown", () => {
         ])
         expect(segments.map(segment => segment.text).join("")).toBe(text)
     })
+
+    it("protects linear URLs when requested", () => {
+        const text = "linear://workspace/issue/ACME-123"
+        const segments = segmentMarkdown(text, {
+            protectUrls: true,
+        })
+
+        expect(segments).toEqual([
+            {
+                kind: "protected",
+                protectedKind: "url",
+                start: 0,
+                end: text.length,
+                text,
+            },
+        ])
+    })
 })
 
 describe("mapMarkdownProse", () => {
diff --git a/src/markdown-segments.ts b/src/markdown-segments.ts
index c0a37c9..37e9a62 100644
--- a/src/markdown-segments.ts
+++ b/src/markdown-segments.ts
@@ -138,7 +138,7 @@ const buildProtectedPattern = (protectUrls: boolean): RegExp => {
     ]
 
     if (protectUrls) {
-        parts.push("https?:\\/\\/[^\\s]+")
+        parts.push("(?:https?:\\/\\/|linear:\\/\\/)[^\\s]+")
     }
 
     return new RegExp(`(${parts.join("|")})`, "g")
diff --git a/src/replace-urls/__tests__/replace-urls.test.ts b/src/replace-urls/__tests__/replace-urls.test.ts
index fbf68d6..e6684b5 100644
--- a/src/replace-urls/__tests__/replace-urls.test.ts
+++ b/src/replace-urls/__tests__/replace-urls.test.ts
@@ -22,6 +22,14 @@ describe("replace-urls", () => {
         )
     })
 
+    it("does not rewrite https URLs inside wikilinks", () => {
+        const input = "[[https://github.com/kdnk/obsidian-automatic-linker]]"
+
+        expect(
+            replaceURLs(input, baseSettings, formatGitHubURL),
+        ).toBe(input)
+    })
+
     it("should replace linear protocol URLs", () => {
         const input = "linear://workspace/issue/ACME-123"
         const expected
@@ -39,6 +47,21 @@ describe("replace-urls", () => {
         ).toBe(expected)
     })
 
+    it("does not rewrite linear protocol URLs inside wikilinks", () => {
+        const input = "[[linear://workspace/issue/ACME-123]]"
+
+        expect(
+            replaceURLs(
+                input,
+                {
+                    ...baseSettings,
+                    formatLinearURLs: true,
+                },
+                formatLinearURL,
+            ),
+        ).toBe(input)
+    })
+
     it("keeps raw helper semantics inside Markdown links and angle autolinks", () => {
         const input = [
             "[label](https://github.com/kdnk/obsidian-automatic-linker)",
diff --git a/src/replace-urls/replace-urls.ts b/src/replace-urls/replace-urls.ts
index 75f5c63..5587d41 100644
--- a/src/replace-urls/replace-urls.ts
+++ b/src/replace-urls/replace-urls.ts
@@ -1,9 +1,39 @@
 import { AutomaticLinkerSettings } from "../settings/settings-info"
 
 const URL_PATTERN = /(?:https?:\/\/|linear:\/\/)[^\s<>\]]+/g
+const WIKILINK_PATTERN = /\[\[[\s\S]*?\]\]/g
+
+const collectWikilinkRanges = (text: string): Array<{ start: number, end: number }> => {
+    const ranges: Array<{ start: number, end: number }> = []
+    let match: RegExpExecArray | null
+
+    while ((match = WIKILINK_PATTERN.exec(text)) !== null) {
+        ranges.push({
+            start: match.index,
+            end: match.index + match[0].length,
+        })
+    }
+
+    return ranges
+}
+
+const isInsideRange = (
+    index: number,
+    ranges: Array<{ start: number, end: number }>,
+): boolean => ranges.some(range => index >= range.start && index < range.end)
 
 export const replaceURLs = (
     fileContent: string,
     settings: AutomaticLinkerSettings,
     formatter: (url: string, settings: AutomaticLinkerSettings) => string,
-) => fileContent.replace(URL_PATTERN, match => formatter(match, settings))
+) => {
+    const wikilinkRanges = collectWikilinkRanges(fileContent)
+
+    return fileContent.replace(URL_PATTERN, (match, offset) => {
+        if (isInsideRange(offset, wikilinkRanges)) {
+            return match
+        }
+
+        return formatter(match, settings)
+    })
+}