diff --git a/apps/web/src/components/code-reviews/ReviewConfigForm.tsx b/apps/web/src/components/code-reviews/ReviewConfigForm.tsx
index 0e5875052d..81297cb529 100644
--- a/apps/web/src/components/code-reviews/ReviewConfigForm.tsx
+++ b/apps/web/src/components/code-reviews/ReviewConfigForm.tsx
@@ -454,7 +454,7 @@ export function ReviewConfigForm({
         platform,
         reviewStyle,
         focusAreas,
-        customInstructions: customInstructions.trim() || undefined,
+        customInstructions: customInstructions || undefined,
         modelSlug: selectedModel,
         thinkingEffort,
         gateThreshold,
@@ -470,7 +470,7 @@ export function ReviewConfigForm({
         platform,
         reviewStyle,
         focusAreas,
-        customInstructions: customInstructions.trim() || undefined,
+        customInstructions: customInstructions || undefined,
         modelSlug: selectedModel,
         thinkingEffort,
         gateThreshold,
@@ -1047,18 +1047,30 @@ export function ReviewConfigForm({
 
             {/* Custom Instructions */}
             <div className="space-y-3">
-              <Label htmlFor="custom-instructions">Custom Instructions (Optional)</Label>
+              <Label htmlFor="custom-instructions">Custom Instructions (Deprecated)</Label>
               <Textarea
                 id="custom-instructions"
-                placeholder="e.g., 'Always check for TypeScript strict mode compliance' or 'Focus on React best practices'"
                 value={customInstructions}
-                onChange={e => setCustomInstructions(e.target.value)}
                 rows={4}
                 className="resize-none"
+                disabled
+                aria-describedby="custom-instructions-deprecation"
               />
-              <p className="text-muted-foreground text-sm">
-                Add specific guidelines for your team's code review standards
-              </p>
+              <Alert id="custom-instructions-deprecation" variant="warning">
+                <AlertCircle className="size-4" />
+                <AlertTitle>Custom instructions are no longer applied</AlertTitle>
+                <AlertDescription>
+                  This value remains visible to help you migrate it, but Code Reviewer no longer
+                  uses it. Move any guidance you still need to a REVIEW.md file in the repository
+                  root.{' '}
+                  <Link
+                    href={reviewMdGuideHref}
+                    className="text-blue-400 underline-offset-4 hover:text-blue-300 hover:underline"
+                  >
+                    Learn about REVIEW.md
+                  </Link>
+                </AlertDescription>
+              </Alert>
             </div>
 
             {/* Save Button */}
diff --git a/apps/web/src/components/code-reviews/ReviewMdGuideContent.tsx b/apps/web/src/components/code-reviews/ReviewMdGuideContent.tsx
index f22926fab5..33d153b01c 100644
--- a/apps/web/src/components/code-reviews/ReviewMdGuideContent.tsx
+++ b/apps/web/src/components/code-reviews/ReviewMdGuideContent.tsx
@@ -27,7 +27,7 @@ const guidanceItems = [
 
 const limits = [
   'Hard safety, tooling, platform, and read-only constraints still apply.',
-  'Custom instructions and focus areas are still applied around repository guidance.',
+  'Focus areas are still applied around repository guidance.',
   '@ imports are not expanded. Keep the guidance directly in REVIEW.md.',
   'Content is truncated after 10,000 characters.',
   'Do not include secrets, credentials, tokens, or private operational data.',
diff --git a/apps/web/src/lib/code-reviews/prompts/generate-prompt.test.ts b/apps/web/src/lib/code-reviews/prompts/generate-prompt.test.ts
index f984af992a..9b1733af40 100644
--- a/apps/web/src/lib/code-reviews/prompts/generate-prompt.test.ts
+++ b/apps/web/src/lib/code-reviews/prompts/generate-prompt.test.ts
@@ -138,10 +138,12 @@ describe('resolveTemplate', () => {
 
 // --- generateReviewPrompt (integration) ---
 
+const legacyCustomInstructions = 'Also consider account-level policy.';
+
 const baseConfig = {
   review_style: 'balanced' as const,
   focus_areas: [],
-  custom_instructions: '',
+  custom_instructions: legacyCustomInstructions,
   model_slug: 'test-model',
 } satisfies CodeReviewAgentConfig;
 
@@ -152,6 +154,8 @@ describe('generateReviewPrompt', () => {
     expect(prompt).toContain('# WHAT TO REVIEW');
     expect(prompt).toContain('Security vulnerabilities (injection, XSS, auth bypass)');
     expect(prompt).not.toContain(`# ${REVIEW_INSTRUCTIONS_FILE} code review instructions`);
+    expect(prompt).not.toContain('# CUSTOM INSTRUCTIONS');
+    expect(prompt).not.toContain(legacyCustomInstructions);
   });
 
   it('replaces built-in review guidance with REVIEW.md instructions at the same prompt point', async () => {
@@ -164,7 +168,6 @@ describe('generateReviewPrompt', () => {
     ].join('\n');
     const customConfig = {
       ...baseConfig,
-      custom_instructions: 'Also consider account-level policy.',
       focus_areas: ['security'],
     } satisfies CodeReviewAgentConfig;
 
@@ -172,8 +175,8 @@ describe('generateReviewPrompt', () => {
       repositoryReviewInstructions,
     });
 
-    expect(prompt).toContain('# CUSTOM INSTRUCTIONS');
-    expect(prompt).toContain('Also consider account-level policy.');
+    expect(prompt).not.toContain('# CUSTOM INSTRUCTIONS');
+    expect(prompt).not.toContain(legacyCustomInstructions);
     expect(prompt).toContain(`# ${REVIEW_INSTRUCTIONS_FILE} code review instructions`);
     expect(prompt).toContain('Only flag regressions with direct evidence.');
     expect(prompt).toContain('```ts\nconst markdown = true;\n```');
@@ -185,9 +188,6 @@ describe('generateReviewPrompt', () => {
     expect(prompt).toContain('# COMMENT FORMAT');
     expect(prompt).toContain('## Inline Comments API Call');
 
-    expect(prompt.indexOf('# CUSTOM INSTRUCTIONS')).toBeLessThan(
-      prompt.indexOf(`# ${REVIEW_INSTRUCTIONS_FILE} code review instructions`)
-    );
     expect(prompt.indexOf(`# ${REVIEW_INSTRUCTIONS_FILE} code review instructions`)).toBeLessThan(
       prompt.indexOf('# FOCUS AREAS')
     );
diff --git a/apps/web/src/lib/code-reviews/prompts/generate-prompt.ts b/apps/web/src/lib/code-reviews/prompts/generate-prompt.ts
index 5877d6a437..582fb73488 100644
--- a/apps/web/src/lib/code-reviews/prompts/generate-prompt.ts
+++ b/apps/web/src/lib/code-reviews/prompts/generate-prompt.ts
@@ -9,7 +9,7 @@
  * 4. Adding dynamic context (existing comments table)
  * 5. Selecting CREATE vs UPDATE summary command
  * 6. Platform-specific template selection (GitHub vs GitLab)
- * 7. Injecting style guidance, custom instructions, and focus areas from config
+ * 7. Injecting style guidance and focus areas from config
  * 8. Applying per-style comment format and summary format overrides
  */
 
@@ -22,7 +22,6 @@ import { logExceptInTest } from '@/lib/utils.server';
 import type { CodeReviewPlatform } from '@/lib/code-reviews/core/schemas';
 import { getPromptTemplateFeatureFlag, getPlatformConfig } from './platform-helpers';
 import { PLATFORM } from '@/lib/integrations/core/constants';
-import { sanitizeUserInput } from './prompt-utils';
 import { formatRepositoryReviewInstructions } from './repository-review-instructions';
 import { getCurrentReviewSummaryForContext } from '../summary/history';
 
@@ -263,15 +262,10 @@ export async function generateReviewPrompt(
     prompt += styleGuide + '\n\n';
   }
 
-  // 3. Custom instructions (user-provided, sanitized to prevent injection)
-  if (config.custom_instructions) {
-    prompt += '# CUSTOM INSTRUCTIONS\n\n' + sanitizeUserInput(config.custom_instructions) + '\n\n';
-  }
-
-  // 4. Hard constraints (MOST IMPORTANT - always included)
+  // 3. Hard constraints (MOST IMPORTANT - always included)
   prompt += template.hardConstraints + '\n\n';
 
-  // 5. Workflow with placeholders replaced
+  // 4. Workflow with placeholders replaced
   // Use incremental workflow when we have a previous completed review SHA and a summary comment
   if (
     previousHeadSha &&
@@ -305,19 +299,19 @@ export async function generateReviewPrompt(
     }
   }
 
-  // 6. What to review
+  // 5. What to review
   prompt +=
     (repositoryReviewInstructions
       ? formatRepositoryReviewInstructions(repositoryReviewInstructions)
       : template.whatToReview) + '\n\n';
 
-  // 7. Focus areas (if any selected)
+  // 6. Focus areas (if any selected)
   if (config.focus_areas.length > 0) {
     prompt +=
       '# FOCUS AREAS\n\nPay special attention to: ' + config.focus_areas.join(', ') + '\n\n';
   }
 
-  // 8. Comment format (use style override if available, otherwise default)
+  // 7. Comment format (use style override if available, otherwise default)
   const commentFormat = template.commentFormatOverrides?.[reviewStyle] ?? template.commentFormat;
   prompt += commentFormat + '\n\n';
 
@@ -325,7 +319,7 @@ export async function generateReviewPrompt(
     prompt += template.inlineCommentFooter + '\n\n';
   }
 
-  // 9. Dynamic context section (separator)
+  // 8. Dynamic context section (separator)
   prompt += '---\n\n# CONTEXT FOR THIS ' + platformConfig.prTerm + '\n\n';
   prompt += `**${platform === PLATFORM.GITLAB ? 'Project' : 'Repository'}:** ${repository}\n`;
   prompt += `**${platformConfig.prTerm} Number:** ${pr}\n\n`;