diff --git a/src/__tests__/main-link-generator.test.ts b/src/__tests__/main-link-generator.test.ts
new file mode 100644
index 0000000..807d9b6
--- /dev/null
+++ b/src/__tests__/main-link-generator.test.ts
@@ -0,0 +1,79 @@
+import { describe, expect, it, vi } from "vitest"
+import { buildCandidateTrieForTest } from "../replace-links/__tests__/test-helpers"
+import { DEFAULT_SETTINGS } from "../settings/settings-info"
+
+class MockTFile {
+    path: string
+
+    constructor(path: string) {
+        this.path = path
+    }
+}
+
+vi.mock("obsidian", () => ({
+    App: class {},
+    Editor: class {},
+    getFrontMatterInfo: () => ({ contentStart: 0 }),
+    MarkdownView: class {},
+    Notice: class {},
+    parseFrontMatterAliases: () => [],
+    Plugin: class {
+        app: unknown
+
+        constructor(app: unknown) {
+            this.app = app
+        }
+    },
+    PluginSettingTab: class {},
+    request: async () => ({}),
+    Setting: class {
+        setName() { return this }
+        setDesc() { return this }
+        setHeading() { return this }
+        addToggle() { return this }
+        addTextArea() { return this }
+    },
+    TFile: MockTFile,
+}))
+
+describe("AutomaticLinkerPlugin link generator", () => {
+    it("escapes alias separators generated by Obsidian inside markdown tables", async () => {
+        const { default: AutomaticLinkerPlugin } = await import("../main")
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+            ignoreCase: true,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "notes/foo", aliases: ["bar"] }],
+            settings,
+        })
+        const targetFile = new MockTFile("notes/foo.md")
+        const app = {
+            fileManager: {
+                generateMarkdownLink: vi.fn(() => "[[notes/foo|bar]]"),
+            },
+            vault: {
+                getAbstractFileByPath: vi.fn((path: string) => {
+                    if (path === "notes/foo.md") return targetFile
+                    return null
+                }),
+                getConfig: vi.fn(),
+            },
+        }
+        const plugin = new AutomaticLinkerPlugin(app as never, {} as never)
+        plugin.settings = {
+            ...DEFAULT_SETTINGS,
+            formatGitHubURLs: false,
+            formatJiraURLs: false,
+            replaceUrlWithTitle: false,
+            respectNewFileFolderPath: false,
+        }
+        ;(plugin as unknown as { trie: typeof trie }).trie = trie
+        ;(plugin as unknown as { candidateMap: typeof candidateMap }).candidateMap = candidateMap
+
+        const result = plugin.modifyLinks("| bar | x |\n| --- | --- |\n", "current-file.md")
+
+        expect(result).toBe("| [[notes/foo\\|bar]] | x |\n| --- | --- |\n")
+    })
+})
diff --git a/src/main.ts b/src/main.ts
index d008001..ba87f72 100644
--- a/src/main.ts
+++ b/src/main.ts
@@ -77,7 +77,10 @@ export default class AutomaticLinkerPlugin extends Plugin {
             if (targetFile instanceof TFile) {
                 // File exists, use Obsidian's generateMarkdownLink API
                 try {
-                    const link = this.app.fileManager.generateMarkdownLink(targetFile, sourcePath, "", alias || "")
+                    let link = this.app.fileManager.generateMarkdownLink(targetFile, sourcePath, "", alias || "")
+                    if (isInTable && link.includes("|")) {
+                        link = link.replace(/\|/g, "\\|")
+                    }
                     return link
                 }
                 catch (error) {