diff --git a/src/consts.ts b/src/consts.ts
index 76fd024..78dfaa6 100644
--- a/src/consts.ts
+++ b/src/consts.ts
@@ -44,5 +44,8 @@ export const KNOWN_BOT_USERS: readonly string[] = [
 // Excludes the team from correct linking and estimate checks.
 export const SKIP_LINKING_AND_ESTIMATE_CHECKS_FOR_TEAMS: readonly string[] = ['Docs'];
 
+// Error returned by the `addCloseIssueReferences` mutation when the issue has too many manually linked pull requests.
+export const MANUAL_REFERENCE_LIMIT_ERROR_MESSAGE = 'Issue exceeds manual reference limit';
+
 export const LINKING_CHECK_RETRIES = 8;
 export const LINKING_CHECK_DELAY_MILLIS = 15 * 1000;
diff --git a/src/pull_request_toolkit.ts b/src/pull_request_toolkit.ts
index 001142b..4d03f9d 100644
--- a/src/pull_request_toolkit.ts
+++ b/src/pull_request_toolkit.ts
@@ -2,6 +2,7 @@ import {
     PROJECT_FIELD_NAMES,
     KNOWN_BOT_USERS,
     LABELS,
+    MANUAL_REFERENCE_LIMIT_ERROR_MESSAGE,
     PRODUCT_ENGINEERING_TEAM_SLUG,
     TEAM_LABEL_PREFIX,
     TEAM_NAME_TO_LABEL,
@@ -512,7 +513,21 @@ export class PullRequestToolkit {
         const mentionedIssues = await this.getIssuesMentionedInPullRequestBody();
 
         // Native references are linked automatically by GitHub
-        const issuesToLink = mentionedIssues.filter((issue) => !issue.isNativeReference);
+        const nonNativeReferences = mentionedIssues.filter((issue) => !issue.isNativeReference);
+        if (nonNativeReferences.length === 0) return;
+
+        const alreadyLinkedIssues = await this.githubModel.getNativelyLinkedIssuesForPullRequest(
+            this.pullRequestRepoOwner,
+            this.pullRequestRepoName,
+            this.pullRequestNumber,
+        );
+        const issuesToLink = this.deduplicateIssues(nonNativeReferences).filter(
+            (issue) =>
+                !alreadyLinkedIssues.some(
+                    (linked) =>
+                        linked.owner === issue.owner && linked.repo === issue.repo && linked.number === issue.number,
+                ),
+        );
         if (issuesToLink.length === 0) return;
 
         const pullRequest = await this.getPullRequest();
@@ -523,7 +538,19 @@ export class PullRequestToolkit {
                 issueReference.repo,
                 issueReference.number,
             );
-            await this.githubModel.linkPullRequestToIssue(issue.node_id, pullRequest.node_id);
+            try {
+                await this.githubModel.linkPullRequestToIssue(issue.node_id, pullRequest.node_id);
+            } catch (error) {
+                // GitHub allows only a limited number of manually linked pull requests per issue. The link only
+                // affects the issue's Development sidebar; the linking check reads the body references directly.
+                if (error instanceof Error && error.message.includes(MANUAL_REFERENCE_LIMIT_ERROR_MESSAGE)) {
+                    this.core.warning(
+                        `Could not link issue ${issueReference.owner}/${issueReference.repo}#${issueReference.number}, it already has the maximum number of manually linked pull requests.`,
+                    );
+                    continue;
+                }
+                throw error;
+            }
         }
 
         this.core.info('Linked issues mentioned in the pull request body.');
diff --git a/tests/pull_request_toolkit.test.ts b/tests/pull_request_toolkit.test.ts
index 263bfc2..b38f3e1 100644
--- a/tests/pull_request_toolkit.test.ts
+++ b/tests/pull_request_toolkit.test.ts
@@ -7,6 +7,7 @@ import type { Core } from '../src/types.ts';
 
 const mockCore = {
     info: vi.fn(),
+    warning: vi.fn(),
     error: vi.fn(),
 } as unknown as Core;
 
@@ -107,3 +108,59 @@ describe('isCorrectlyLinkedAndEstimated', () => {
         expect(isEstimated).toBe(false);
     });
 });
+
+describe('linkIssuesMentionedInPullRequestBody', () => {
+    const partOfPullRequest = { ...basePullRequest, node_id: 'PR_1', body: 'Part of #100\nPart of #200' };
+
+    function makeLinkingGithubModel(overrides: Partial<GitHubModel> = {}) {
+        return makeGithubModel({
+            getPullRequest: vi.fn().mockResolvedValue(partOfPullRequest),
+            getIssue: vi
+                .fn()
+                .mockImplementation((_owner: string, _repo: string, number: number) =>
+                    Promise.resolve({ node_id: `I_${number}` }),
+                ),
+            linkPullRequestToIssue: vi.fn().mockResolvedValue({}),
+            ...overrides,
+        });
+    }
+
+    test('skips issues that are already linked', async () => {
+        const githubModel = makeLinkingGithubModel({
+            getNativelyLinkedIssuesForPullRequest: vi
+                .fn()
+                .mockResolvedValue([{ owner: 'apify', repo: 'apify-proxy', number: 100 }]),
+        });
+
+        await makeToolkit(githubModel).linkIssuesMentionedInPullRequestBody();
+
+        expect(githubModel.linkPullRequestToIssue).toHaveBeenCalledTimes(1);
+        expect(githubModel.linkPullRequestToIssue).toHaveBeenCalledWith('I_200', 'PR_1');
+    });
+
+    test('continues with a warning when an issue exceeds the manual reference limit', async () => {
+        const githubModel = makeLinkingGithubModel({
+            linkPullRequestToIssue: vi
+                .fn()
+                .mockRejectedValueOnce(
+                    new Error(
+                        'Request failed due to following response errors:\n - Issue exceeds manual reference limit',
+                    ),
+                )
+                .mockResolvedValueOnce({}),
+        });
+
+        await expect(makeToolkit(githubModel).linkIssuesMentionedInPullRequestBody()).resolves.toBeUndefined();
+
+        expect(githubModel.linkPullRequestToIssue).toHaveBeenCalledTimes(2);
+        expect(mockCore.warning).toHaveBeenCalledWith(expect.stringContaining('apify/apify-proxy#100'));
+    });
+
+    test('rethrows other linking errors', async () => {
+        const githubModel = makeLinkingGithubModel({
+            linkPullRequestToIssue: vi.fn().mockRejectedValue(new Error('Something else')),
+        });
+
+        await expect(makeToolkit(githubModel).linkIssuesMentionedInPullRequestBody()).rejects.toThrow('Something else');
+    });
+});