diff --git a/.changeset/calm-fences-preserve.md b/.changeset/calm-fences-preserve.md
new file mode 100644
index 0000000000..2115a8ce6f
--- /dev/null
+++ b/.changeset/calm-fences-preserve.md
@@ -0,0 +1,7 @@
+---
+"@fission-ai/openspec": patch
+---
+
+### Bug Fixes
+
+- Preserve internal literal blank-line runs in backtick- and tilde-fenced code blocks when applying unrelated spec changes.
diff --git a/src/core/specs-apply.ts b/src/core/specs-apply.ts
index 81d5516cf4..a00fd8ee60 100644
--- a/src/core/specs-apply.ts
+++ b/src/core/specs-apply.ts
@@ -561,11 +561,11 @@ export async function buildUpdatedSpec(
   // glued the heading to the Purpose paragraph and the first requirement, so
   // every archive rewrote a well-formatted spec into that shape. Separate
   // non-empty slices with one blank line instead.
-  const rebuilt = [parts.before.trimEnd(), parts.headerLine, reqBody, parts.after.trim()]
-    .filter((s) => s !== '')
-    .join('\n\n')
-    .replace(/\n{3,}/g, '\n\n')
-    .trimEnd() + '\n';
+  const rebuilt = collapseExcessiveBlankLinesOutsideFences(
+    [parts.before.trimEnd(), parts.headerLine, reqBody, parts.after.trim()]
+      .filter((s) => s !== '')
+      .join('\n\n')
+  ).trimEnd() + '\n';
 
   return {
     rebuilt,
@@ -586,6 +586,32 @@ export async function buildUpdatedSpec(
   };
 }
 
+/**
+ * Match the serializer's established blank-line collapse outside code fences
+ * while preserving runs of literal empty lines inside recognized fences.
+ */
+function collapseExcessiveBlankLinesOutsideFences(content: string): string {
+  const lines = content.split('\n');
+  const fenceMask = buildCodeFenceMask(lines);
+  const output = [lines[0] ?? ''];
+  let consecutiveOutsideNewlines = 0;
+
+  for (let index = 1; index < lines.length; index++) {
+    const insideFence = fenceMask[index - 1] && fenceMask[index];
+    if (insideFence || consecutiveOutsideNewlines < 2) {
+      output.push('\n');
+    }
+
+    consecutiveOutsideNewlines = insideFence ? 0 : consecutiveOutsideNewlines + 1;
+    output.push(lines[index]);
+    if (lines[index] !== '') {
+      consecutiveOutsideNewlines = 0;
+    }
+  }
+
+  return output.join('');
+}
+
 /**
  * The suffix of a requirement block that begins with content the requirement
  * parser did not recognize as a boundary: a `#`, `##`, or `###` heading after
diff --git a/test/core/specs-apply.serialization.test.ts b/test/core/specs-apply.serialization.test.ts
index 3edad0260c..ba19f0e4ee 100644
--- a/test/core/specs-apply.serialization.test.ts
+++ b/test/core/specs-apply.serialization.test.ts
@@ -129,4 +129,69 @@ describe('spec serialization', () => {
       'serializer output.\n\n## Requirements\n\n### Requirement: Existing behavior'
     );
   });
+
+  it('preserves internal blank-line runs in untouched fences while collapsing prose', async () => {
+    const fencedSpec = [
+      '# demo Specification',
+      '',
+      '## Purpose',
+      'Purpose prose before.',
+      '',
+      '',
+      '',
+      'Purpose prose after.',
+      '',
+      '```text',
+      'purpose fence before',
+      '',
+      '',
+      'purpose fence after',
+      '```',
+      '',
+      '## Requirements',
+      ORIGINAL_REQUIREMENT,
+      '',
+      '### Requirement: Untouched fenced example',
+      'The project SHALL preserve fenced examples.',
+      '',
+      '',
+      '~~~text',
+      'requirement fence before',
+      '',
+      '',
+      'requirement fence after',
+      '~~~',
+      '',
+      '',
+      '#### Scenario: Untouched path',
+      '- **WHEN** an unrelated requirement is updated',
+      '- **THEN** the fenced example SHALL keep its internal blank lines',
+      '',
+      'Whitespace-only prose boundary.',
+      '   ',
+      '',
+      '',
+      'Whitespace-only prose after.',
+      '',
+    ].join('\n');
+
+    const result = await build(fencedSpec);
+
+    expect(result.counts.modified).toBe(1);
+    expect(result.rebuilt).toContain('The project SHALL expose the updated behavior.');
+    expect(result.rebuilt).toContain(
+      '```text\npurpose fence before\n\n\npurpose fence after\n```'
+    );
+    expect(result.rebuilt).toContain(
+      '~~~text\nrequirement fence before\n\n\nrequirement fence after\n~~~'
+    );
+    expect(result.rebuilt).toContain('fenced examples.\n\n~~~text');
+    expect(result.rebuilt).toContain('~~~\n\n#### Scenario: Untouched path');
+    expect(result.rebuilt).toContain('Purpose prose before.\n\nPurpose prose after.');
+    expect(result.rebuilt).not.toContain('Purpose prose before.\n\n\nPurpose prose after.');
+    expect(result.rebuilt).toContain(
+      'Whitespace-only prose boundary.\n   \n\nWhitespace-only prose after.'
+    );
+    expectOneFinalLf(result.rebuilt);
+  });
 });