diff --git a/src/browser/stories/App.markdown.stories.tsx b/src/browser/stories/App.markdown.stories.tsx
index 96605cef21..6b39ad2d71 100644
--- a/src/browser/stories/App.markdown.stories.tsx
+++ b/src/browser/stories/App.markdown.stories.tsx
@@ -4,6 +4,20 @@
 
 import { appMeta, AppWithMocks, type AppStory } from "./meta.js";
 import { STABLE_TIMESTAMP, createUserMessage, createAssistantMessage } from "./mockFactory";
+import { expect, waitFor } from "@storybook/test";
+
+async function waitForChatMessagesLoaded(canvasElement: HTMLElement): Promise<void> {
+  await waitFor(
+    () => {
+      const messageWindow = canvasElement.querySelector('[data-testid="message-window"]');
+      if (!messageWindow || messageWindow.getAttribute("data-loaded") !== "true") {
+        throw new Error("Messages not loaded yet");
+      }
+    },
+    { timeout: 5000 }
+  );
+}
+
 import { setupSimpleChatStory } from "./storyHelpers";
 
 export default {
@@ -87,6 +101,18 @@ describe('getUser', () => {
     expect(res.status).toBe(401);
   });
 });
+\`\`\`
+
+Text code blocks (regression: no phantom trailing blank line after highlighting):
+
+\`\`\`text
+https://github.com/coder/mux/pull/new/chat-autocomplete-b24r
+\`\`\`
+
+Code blocks without language (regression: avoid extra vertical spacing):
+
+\`\`\`
+65d02772b 🤖 feat: Settings-driven model selector with visibility controls
 \`\`\``;
 
 // ═══════════════════════════════════════════════════════════════════════════════
@@ -160,4 +186,56 @@ export const CodeBlocks: AppStory = {
       }
     />
   ),
+  play: async ({ canvasElement }: { canvasElement: HTMLElement }) => {
+    await waitForChatMessagesLoaded(canvasElement);
+
+    const url = "https://github.com/coder/mux/pull/new/chat-autocomplete-b24r";
+
+    // Find the highlighted code block containing the URL.
+    const container = await waitFor(
+      () => {
+        const candidates = Array.from(canvasElement.querySelectorAll(".code-block-container"));
+        const found = candidates.find((el) => el.textContent?.includes(url));
+        if (!found) {
+          throw new Error("URL code block not found");
+        }
+        return found;
+      },
+      { timeout: 5000 }
+    );
+
+    // Ensure we capture the post-highlight DOM (Shiki wraps tokens in spans).
+    await waitFor(
+      () => {
+        const hasHighlightedSpans = container.querySelector(".code-line span");
+        if (!hasHighlightedSpans) {
+          throw new Error("Code block not highlighted yet");
+        }
+      },
+      { timeout: 5000 }
+    );
+
+    const noLangLine = "65d02772b 🤖 feat: Settings-driven model selector with visibility controls";
+
+    const codeEl = await waitFor(
+      () => {
+        const candidates = Array.from(
+          canvasElement.querySelectorAll(".markdown-content pre > code")
+        );
+        const found = candidates.find((el) => el.textContent?.includes(noLangLine));
+        if (!found) {
+          throw new Error("No-language code block not found");
+        }
+        return found;
+      },
+      { timeout: 5000 }
+    );
+
+    const style = window.getComputedStyle(codeEl);
+    await expect(style.marginTop).toBe("0px");
+    await expect(style.marginBottom).toBe("0px");
+    // Regression: Shiki can emit a visually-empty trailing line (<span></span>), which would render
+    // as a phantom extra line in our line-numbered code blocks.
+    await expect(container.querySelectorAll(".line-number").length).toBe(1);
+  },
 };
diff --git a/src/browser/styles/globals.css b/src/browser/styles/globals.css
index d2f7aaa272..da3076c391 100644
--- a/src/browser/styles/globals.css
+++ b/src/browser/styles/globals.css
@@ -1414,7 +1414,7 @@ code {
 }
 
 .markdown-content pre {
-  background: rgba(0, 0, 0, 0.3);
+  background: var(--color-code-bg);
   padding: 12px;
   border-radius: 4px;
   overflow-x: auto;
@@ -1424,6 +1424,7 @@ code {
 .markdown-content pre code {
   background: none;
   padding: 0;
+  margin: 0;
   color: var(--color-foreground);
 }
 
diff --git a/src/browser/utils/highlighting/shiki-shared.test.ts b/src/browser/utils/highlighting/shiki-shared.test.ts
new file mode 100644
index 0000000000..53de593d5b
--- /dev/null
+++ b/src/browser/utils/highlighting/shiki-shared.test.ts
@@ -0,0 +1,15 @@
+import { describe, expect, test } from "bun:test";
+
+import { extractShikiLines } from "./shiki-shared";
+
+describe("extractShikiLines", () => {
+  test("removes trailing visually-empty Shiki line (e.g. <span></span>)", () => {
+    const html = `<pre class="shiki"><code><span class="line"><span style="color:#fff">https://github.com/coder/mux/pull/new/chat-autocomplete-b24r</span></span>
+<span class="line"><span style="color:#fff"></span></span>
+</code></pre>`;
+
+    expect(extractShikiLines(html)).toEqual([
+      `<span style="color:#fff">https://github.com/coder/mux/pull/new/chat-autocomplete-b24r</span>`,
+    ]);
+  });
+});
diff --git a/src/browser/utils/highlighting/shiki-shared.ts b/src/browser/utils/highlighting/shiki-shared.ts
index 45110e64c6..805a2d48c4 100644
--- a/src/browser/utils/highlighting/shiki-shared.ts
+++ b/src/browser/utils/highlighting/shiki-shared.ts
@@ -24,6 +24,19 @@ export function mapToShikiLang(detectedLang: string): string {
  * Extract line contents from Shiki HTML output
  * Shiki wraps code in <pre><code>...</code></pre> with <span class="line">...</span> per line
  */
+function isVisuallyEmptyShikiLine(lineHtml: string): boolean {
+  // Shiki represents an empty line as something like:
+  //   <span class="line"><span style="..."></span></span>
+  // which is visually empty but non-empty as a string.
+  //
+  // We treat these as empty so callers don't render a phantom blank line.
+  const textOnly = lineHtml
+    .replace(/<[^>]*>/g, "")
+    .replace(/&nbsp;/g, "")
+    .trim();
+  return textOnly === "";
+}
+
 export function extractShikiLines(html: string): string[] {
   const codeMatch = /<code[^>]*>(.*?)<\/code>/s.exec(html);
   if (!codeMatch) return [];
@@ -35,10 +48,11 @@ export function extractShikiLines(html: string): string[] {
     const contentStart = start + '<span class="line">'.length;
     const end = chunk.lastIndexOf("</span>");
 
-    return end > contentStart ? chunk.substring(contentStart, end) : "";
+    const lineHtml = end > contentStart ? chunk.substring(contentStart, end) : "";
+    return isVisuallyEmptyShikiLine(lineHtml) ? "" : lineHtml;
   });
 
-  // Remove trailing empty lines (Shiki often adds one)
+  // Remove trailing empty lines (Shiki often adds one).
   while (lines.length > 0 && lines[lines.length - 1] === "") {
     lines.pop();
   }