diff --git a/.changeset/fix-single-tilde-strikethrough.md b/.changeset/fix-single-tilde-strikethrough.md
new file mode 100644
index 0000000..e9a0a5d
--- /dev/null
+++ b/.changeset/fix-single-tilde-strikethrough.md
@@ -0,0 +1,6 @@
+---
+"@silicajs/core": patch
+"@silicajs/assistant": patch
+---
+
+Disable GFM single-tilde strikethrough so `~text~` is not crossed out, matching Obsidian syntax.
diff --git a/packages/assistant/src/ui/message.tsx b/packages/assistant/src/ui/message.tsx
index 23be91e..28a4b76 100644
--- a/packages/assistant/src/ui/message.tsx
+++ b/packages/assistant/src/ui/message.tsx
@@ -43,7 +43,7 @@ export function AssistantMessage({ message, onRetry }: AssistantMessageProps) {
       {message.content ? (
         <div className="prose prose-sm dark:prose-invert min-w-0 max-w-none break-words text-sm">
           <ReactMarkdown
-            remarkPlugins={[remarkGfm]}
+            remarkPlugins={[[remarkGfm, { singleTilde: false }]]}
             components={{ a: MarkdownLink }}
           >
             {message.content}
diff --git a/packages/core/src/pipeline.test.tsx b/packages/core/src/pipeline.test.tsx
index 973b404..9447931 100644
--- a/packages/core/src/pipeline.test.tsx
+++ b/packages/core/src/pipeline.test.tsx
@@ -411,6 +411,19 @@ describe("renderMarkdown", () => {
     expect(html).toContain("<pre");
   }, 15_000);
 
+  it("only treats double tildes as strikethrough", async () => {
+    const result = await renderMarkdown(
+      "~~crossed out~~ and ~not crossed~",
+      testContext("index", ["index"]),
+    );
+
+    const html = renderToStaticMarkup(<>{result.content}</>);
+
+    expect(html).toContain("<del>crossed out</del>");
+    expect(html).toContain("~not crossed~");
+    expect(html).not.toContain("<del>not crossed</del>");
+  }, 15_000);
+
   it("sanitizes raw HTML and escapes OFM-injected labels", async () => {
     const result = await renderMarkdown(
       '[[<img src=x onerror=alert(1)>]]\n\n<script>alert(1)</script>\n\n<img src=x onerror=alert(1)>\n\n<h2 id="raw-id">Raw heading</h2>\n\n<h2 id="footnote-label">User heading</h2>',
diff --git a/packages/core/src/pipeline/index.ts b/packages/core/src/pipeline/index.ts
index 2f5368d..80adb5f 100644
--- a/packages/core/src/pipeline/index.ts
+++ b/packages/core/src/pipeline/index.ts
@@ -37,6 +37,9 @@ import {
   rehypeUnwrapSilicaEmbeds,
 } from "./plugins.js";
 
+/** Obsidian strikethrough uses `~~text~~`; single tildes are subscript, not delete. */
+const remarkGfmOptions = { singleTilde: false } as const;
+
 type MdastNode = {
   type: string;
   value?: string;
@@ -367,7 +370,7 @@ function baseProcessor(context: RenderContext) {
   return unified()
     .use(remarkParse)
     .use(remarkFrontmatter, ["yaml"])
-    .use(remarkGfm)
+    .use(remarkGfm, remarkGfmOptions)
     .use(remarkMath)
     .use(remarkObsidian, { inlineTags: context.tags?.inline ?? true })
     .use(remarkSilicaObsidian, context)
@@ -381,7 +384,7 @@ async function runRemarkObsidian(markdown: string, context: RenderContext) {
   const processor = unified()
     .use(remarkParse)
     .use(remarkFrontmatter, ["yaml"])
-    .use(remarkGfm)
+    .use(remarkGfm, remarkGfmOptions)
     .use(remarkMath)
     .use(remarkObsidian, { inlineTags: context.tags?.inline ?? true })
     .use(remarkSilicaObsidian, context);
@@ -413,7 +416,7 @@ function parsePlainTextMarkdown(markdown: string): MdastNode {
   return unified()
     .use(remarkParse)
     .use(remarkFrontmatter, ["yaml"])
-    .use(remarkGfm)
+    .use(remarkGfm, remarkGfmOptions)
     .use(remarkMath)
     .use(remarkObsidian)
     .parse(markdown) as MdastNode;