diff --git a/ui/src/components/IssueChatThread.tsx b/ui/src/components/IssueChatThread.tsx
index ede1450a2d7..4412153f113 100644
--- a/ui/src/components/IssueChatThread.tsx
+++ b/ui/src/components/IssueChatThread.tsx
@@ -89,6 +89,7 @@ import {
   DropdownMenuTrigger,
 } from "@/components/ui/dropdown-menu";
 import { MarkdownBody } from "./MarkdownBody";
+import { WorkspaceFileMarkdownBody } from "./WorkspaceFileMarkdownBody";
 import { MarkdownEditor, type MentionOption, type MarkdownEditorRef } from "./MarkdownEditor";
 import { Identity } from "./Identity";
 import { InlineEntitySelector, type InlineEntityOption } from "./InlineEntitySelector";
@@ -669,15 +670,14 @@ const IssueChatTextPart = memo(function IssueChatTextPart({ text, recessed }: {
     return <SuccessfulRunHandoffCommentCallout text={text} recessed={recessed} onImageClick={onImageClick} />;
   }
   return (
-    <MarkdownBody
+    <WorkspaceFileMarkdownBody
       className="text-sm leading-6"
       style={recessed ? { opacity: 0.55 } : undefined}
       softBreaks
-      linkWorkspaceFileReferences
       onImageClick={onImageClick}
     >
       {text}
-    </MarkdownBody>
+    </WorkspaceFileMarkdownBody>
   );
 });
 
diff --git a/ui/src/components/MarkdownBody.test.tsx b/ui/src/components/MarkdownBody.test.tsx
index 95098a1b9bd..48b695e8a82 100644
--- a/ui/src/components/MarkdownBody.test.tsx
+++ b/ui/src/components/MarkdownBody.test.tsx
@@ -28,7 +28,6 @@ vi.mock("@/lib/router", () => ({
   }: { children: ReactNode; to: string } & React.ComponentProps<"a">) => (
     <a href={to} {...props}>{children}</a>
   ),
-  useLocation: () => ({ pathname: "/", search: "", hash: "" }),
 }));
 
 vi.mock("../api/issues", () => ({
@@ -534,22 +533,4 @@ describe("MarkdownBody", () => {
     expect(html).toContain('href="/issues/ACME-1"');
   });
 
-  it("renders workspace file refs in inline code as workspace file links when enabled", () => {
-    const html = renderToStaticMarkup(
-      <QueryClientProvider client={new QueryClient()}>
-        <ThemeProvider>
-          <MarkdownBody linkWorkspaceFileReferences>
-            {"Check `ui/src/pages/IssueDetail.tsx:42` please."}
-          </MarkdownBody>
-        </ThemeProvider>
-      </QueryClientProvider>,
-    );
-    expect(html).toContain('data-workspace-file-link="true"');
-    expect(html).toContain("ui/src/pages/IssueDetail.tsx:42");
-  });
-
-  it("does not create workspace file links when the flag is off", () => {
-    const html = renderMarkdown("See `ui/src/pages/IssueDetail.tsx:42` for details.");
-    expect(html).not.toContain("data-workspace-file-link");
-  });
 });
diff --git a/ui/src/components/MarkdownBody.tsx b/ui/src/components/MarkdownBody.tsx
index 100c8ae2761..4d4cb8e7bf7 100644
--- a/ui/src/components/MarkdownBody.tsx
+++ b/ui/src/components/MarkdownBody.tsx
@@ -12,13 +12,7 @@ import { issuesApi } from "../api/issues";
 import { queryKeys } from "../lib/queryKeys";
 import { parseIssueReferenceFromHref, remarkLinkIssueReferences } from "../lib/issue-reference";
 import { remarkSoftBreaks } from "../lib/remark-soft-breaks";
-import {
-  parseWorkspaceFileHref,
-  remarkWorkspaceFileRefs,
-  WORKSPACE_FILE_HREF_PREFIX,
-} from "../lib/remark-workspace-file-refs";
 import { StatusIcon } from "./StatusIcon";
-import { WorkspaceFileLink } from "./WorkspaceFileLink";
 
 interface MarkdownBodyProps {
   children: string;
@@ -32,12 +26,6 @@ interface MarkdownBodyProps {
   wikiLinkRoot?: string;
   /** Optional href resolver for wikilinks. Return null to leave a token as plain text. */
   resolveWikiLinkHref?: (target: string, label: string) => string | null | undefined;
-  /**
-   * When true, auto-link workspace file references inside inline code spans
-   * (e.g. `ui/src/pages/IssueDetail.tsx:42`). Requires a FileViewerProvider
-   * ancestor so that clicking a link opens the viewer.
-   */
-  linkWorkspaceFileReferences?: boolean;
   /** Optional resolver for relative image paths (e.g. within export packages) */
   resolveImageSrc?: (src: string) => string | null;
   /** Called when a user clicks an inline image */
@@ -172,7 +160,6 @@ function extractMermaidSource(children: ReactNode): string | null {
 }
 
 function safeMarkdownUrlTransform(url: string): string {
-  if (url.startsWith(WORKSPACE_FILE_HREF_PREFIX)) return url;
   return parseMentionChipHref(url) ? url : defaultUrlTransform(url);
 }
 
@@ -580,7 +567,6 @@ export function MarkdownBody({
   enableWikiLinks = false,
   wikiLinkRoot,
   resolveWikiLinkHref,
-  linkWorkspaceFileReferences = false,
   resolveImageSrc,
   onImageClick,
 }: MarkdownBodyProps) {
@@ -599,9 +585,6 @@ export function MarkdownBody({
   if (linkIssueReferences) {
     remarkPlugins.push([remarkLinkIssueReferences, { knownPrefixes }]);
   }
-  if (linkWorkspaceFileReferences) {
-    remarkPlugins.push(remarkWorkspaceFileRefs);
-  }
   if (softBreaks) {
     remarkPlugins.push(remarkSoftBreaks);
   }
@@ -653,13 +636,6 @@ export function MarkdownBody({
     a: ({ node: _node, href, style: linkStyle, children: linkChildren, ...anchorProps }) => {
       const dataProps = anchorProps as Record<string, unknown>;
       const isWikiLink = dataProps["data-paperclip-wiki-link"] === "true";
-      if (linkWorkspaceFileReferences) {
-        const workspaceFileRef = parseWorkspaceFileHref(href);
-        if (workspaceFileRef) {
-          return <WorkspaceFileLink workspaceFileRef={workspaceFileRef} />;
-        }
-      }
-
       if (isWikiLink && href && !/^[a-z][a-z\d+.-]*:/i.test(href) && !href.startsWith("//")) {
         return (
           <Link
diff --git a/ui/src/components/WorkspaceFileMarkdownBody.test.tsx b/ui/src/components/WorkspaceFileMarkdownBody.test.tsx
new file mode 100644
index 00000000000..ac8874ca963
--- /dev/null
+++ b/ui/src/components/WorkspaceFileMarkdownBody.test.tsx
@@ -0,0 +1,22 @@
+// @vitest-environment node
+
+import { describe, expect, it } from "vitest";
+import { linkWorkspaceFileInlineCode } from "./WorkspaceFileMarkdownBody";
+
+describe("linkWorkspaceFileInlineCode", () => {
+  it("links workspace file refs in inline code to the current issue file viewer", () => {
+    const markdown = linkWorkspaceFileInlineCode(
+      "Check `ui/src/pages/IssueDetail.tsx:42` please.",
+      "/issues/PAP-1",
+      "?tab=chat",
+      "#comment-1",
+    );
+
+    expect(markdown).toContain("[`ui/src/pages/IssueDetail.tsx:42`](");
+    expect(markdown).toContain("/issues/PAP-1?tab=chat&file=ui%2Fsrc%2Fpages%2FIssueDetail.tsx&line=42#comment-1");
+  });
+
+  it("leaves non-file inline code unchanged", () => {
+    expect(linkWorkspaceFileInlineCode("Run `pnpm test`.", "/issues/PAP-1", "", "")).toBe("Run `pnpm test`.");
+  });
+});
diff --git a/ui/src/components/WorkspaceFileMarkdownBody.tsx b/ui/src/components/WorkspaceFileMarkdownBody.tsx
new file mode 100644
index 00000000000..e3764444a77
--- /dev/null
+++ b/ui/src/components/WorkspaceFileMarkdownBody.tsx
@@ -0,0 +1,62 @@
+import type { MouseEvent } from "react";
+import { useMemo } from "react";
+import { useLocation } from "@/lib/router";
+import { readFileViewerStateFromSearch, useFileViewer, writeFileViewerStateToSearch } from "@/context/FileViewerContext";
+import { parseWorkspaceFileRef } from "@/lib/workspace-file-parser";
+import { MarkdownBody } from "./MarkdownBody";
+
+type MarkdownBodyProps = Parameters<typeof MarkdownBody>[0];
+
+const INLINE_CODE_RE = /`([^`\r\n]+)`/g;
+
+function escapeMarkdownLinkLabel(value: string) {
+  return value.replace(/([\\\]])/g, "\\$1");
+}
+
+export function linkWorkspaceFileInlineCode(markdown: string, currentPathname: string, currentSearch: string, currentHash: string) {
+  return markdown.replace(INLINE_CODE_RE, (token, rawCode: string) => {
+    const ref = parseWorkspaceFileRef(rawCode);
+    if (!ref) return token;
+    const nextSearch = writeFileViewerStateToSearch(currentSearch, {
+      path: ref.path,
+      line: ref.line,
+      column: ref.column,
+      workspace: "auto",
+    });
+    const href = `${currentPathname}${nextSearch}${currentHash}`;
+    return `[\`${escapeMarkdownLinkLabel(ref.raw)}\`](${href})`;
+  });
+}
+
+export function WorkspaceFileMarkdownBody({
+  children,
+  ...props
+}: MarkdownBodyProps) {
+  const location = useLocation();
+  const viewer = useFileViewer();
+  const linkedMarkdown = useMemo(
+    () => linkWorkspaceFileInlineCode(children, location.pathname, location.search, location.hash),
+    [children, location.hash, location.pathname, location.search],
+  );
+
+  const handleClick = (event: MouseEvent<HTMLDivElement>) => {
+    if (!viewer) return;
+    if (event.metaKey || event.ctrlKey || event.shiftKey || event.altKey) return;
+    const anchor = (event.target as HTMLElement | null)?.closest("a");
+    if (!anchor) return;
+
+    const url = new URL(anchor.href, window.location.href);
+    if (url.origin !== window.location.origin || url.pathname !== location.pathname) return;
+    const next = readFileViewerStateFromSearch(url.search);
+    if (!next) return;
+
+    event.preventDefault();
+    viewer.open(next);
+  };
+
+  return (
+    <div onClick={handleClick}>
+      <MarkdownBody {...props}>{linkedMarkdown}</MarkdownBody>
+    </div>
+  );
+}