diff --git a/lib/modules/manager/pip-compile/extract.spec.ts b/lib/modules/manager/pip-compile/extract.spec.ts
index bd45db12fff388..533348a7571c8f 100644
--- a/lib/modules/manager/pip-compile/extract.spec.ts
+++ b/lib/modules/manager/pip-compile/extract.spec.ts
@@ -246,26 +246,32 @@ describe('modules/manager/pip-compile/extract', () => {
   });
 
   it('return sorted package files', async () => {
-    fs.readLocalFile.mockResolvedValueOnce(
-      getSimpleRequirementsFile('pip-compile --output-file=4.txt 3.in', [
-        'foo==1.0.1',
-      ]),
-    );
-    fs.readLocalFile.mockResolvedValueOnce('-r 2.txt\nfoo');
-    fs.readLocalFile.mockResolvedValueOnce(
-      getSimpleRequirementsFile('pip-compile --output-file=2.txt 1.in', [
-        'foo==1.0.1',
-      ]),
-    );
-    fs.readLocalFile.mockResolvedValueOnce('foo');
+    fs.readLocalFile.mockImplementation((name): any => {
+      if (name === '1.in') {
+        return 'foo';
+      } else if (name === '2.txt') {
+        return getSimpleRequirementsFile(
+          'pip-compile --output-file=2.txt 1.in',
+          ['foo==1.0.1'],
+        );
+      } else if (name === '3.in') {
+        return '-r 2.txt\nfoo';
+      } else if (name === '4.txt') {
+        return getSimpleRequirementsFile(
+          'pip-compile --output-file=4.txt 3.in',
+          ['foo==1.0.1'],
+        );
+      }
+      return null;
+    });
 
     const lockFiles = ['4.txt', '2.txt'];
     const packageFiles = await extractAllPackageFiles({}, lockFiles);
     expect(packageFiles).toBeDefined();
     expect(packageFiles?.map((p) => p.packageFile)).toEqual(['1.in', '3.in']);
-    expect(packageFiles?.map((p) => p.lockFiles!.pop())).toEqual([
-      '2.txt',
-      '4.txt',
+    expect(packageFiles?.map((p) => p.lockFiles)).toEqual([
+      ['2.txt', '4.txt'],
+      ['4.txt'],
     ]);
   });
 
@@ -359,4 +365,112 @@ describe('modules/manager/pip-compile/extract', () => {
       'pip-compile: dependency not found in lock file',
     );
   });
+
+  it('handles -r reference to another input file', async () => {
+    fs.readLocalFile.mockImplementation((name): any => {
+      if (name === '1.in') {
+        return 'foo';
+      } else if (name === '2.txt') {
+        return getSimpleRequirementsFile(
+          'pip-compile --output-file=2.txt 1.in',
+          ['foo==1.0.1'],
+        );
+      } else if (name === '3.in') {
+        return '-r 1.in\nfoo';
+      } else if (name === '4.txt') {
+        return getSimpleRequirementsFile(
+          'pip-compile --output-file=4.txt 3.in',
+          ['foo==1.0.1'],
+        );
+      }
+      return null;
+    });
+
+    const lockFiles = ['4.txt', '2.txt'];
+    const packageFiles = await extractAllPackageFiles({}, lockFiles);
+    expect(packageFiles?.map((p) => p.lockFiles)).toEqual([
+      ['2.txt', '4.txt'],
+      ['4.txt'],
+    ]);
+  });
+
+  it('handles transitive -r references', async () => {
+    fs.readLocalFile.mockImplementation((name): any => {
+      if (name === '1.in') {
+        return 'foo';
+      } else if (name === '2.txt') {
+        return getSimpleRequirementsFile(
+          'pip-compile --output-file=2.txt 1.in',
+          ['foo==1.0.1'],
+        );
+      } else if (name === '3.in') {
+        return '-r 1.in\nfoo';
+      } else if (name === '4.txt') {
+        return getSimpleRequirementsFile(
+          'pip-compile --output-file=4.txt 3.in',
+          ['foo==1.0.1'],
+        );
+      } else if (name === '5.in') {
+        return '-r 4.txt\nfoo';
+      } else if (name === '6.txt') {
+        return getSimpleRequirementsFile(
+          'pip-compile --output-file=6.txt 5.in',
+          ['foo==1.0.1'],
+        );
+      }
+      return null;
+    });
+
+    const lockFiles = ['4.txt', '2.txt', '6.txt'];
+    const packageFiles = await extractAllPackageFiles({}, lockFiles);
+    expect(packageFiles?.map((p) => p.lockFiles)).toEqual([
+      ['2.txt', '4.txt', '6.txt'],
+      ['4.txt', '6.txt'],
+      ['6.txt'],
+    ]);
+  });
+
+  it('warns on -r reference to failed file', async () => {
+    fs.readLocalFile.mockImplementation((name): any => {
+      if (name === 'reqs-no-headers.txt') {
+        return Fixtures.get('requirementsNoHeaders.txt');
+      } else if (name === '1.in') {
+        return '-r reqs-no-headers.txt\nfoo';
+      } else if (name === '2.txt') {
+        return getSimpleRequirementsFile(
+          'pip-compile --output-file=2.txt 1.in',
+          ['foo==1.0.1'],
+        );
+      }
+      return null;
+    });
+
+    const lockFiles = ['reqs-no-headers.txt', '2.txt'];
+    const packageFiles = await extractAllPackageFiles({}, lockFiles);
+    expect(packageFiles?.map((p) => p.lockFiles)).toEqual([['2.txt']]);
+    expect(logger.warn).toHaveBeenCalledWith(
+      'pip-compile: 1.in references reqs-no-headers.txt which does not appear to be a requirements file managed by pip-compile',
+    );
+  });
+
+  it('warns on -r reference to requirements file not managed by pip-compile', async () => {
+    fs.readLocalFile.mockImplementation((name): any => {
+      if (name === '1.in') {
+        return '-r unmanaged-file.txt\nfoo';
+      } else if (name === '2.txt') {
+        return getSimpleRequirementsFile(
+          'pip-compile --output-file=2.txt 1.in',
+          ['foo==1.0.1'],
+        );
+      }
+      return null;
+    });
+
+    const lockFiles = ['2.txt'];
+    const packageFiles = await extractAllPackageFiles({}, lockFiles);
+    expect(packageFiles?.map((p) => p.lockFiles)).toEqual([['2.txt']]);
+    expect(logger.warn).toHaveBeenCalledWith(
+      'pip-compile: 1.in references unmanaged-file.txt which does not appear to be a requirements file managed by pip-compile',
+    );
+  });
 });
diff --git a/lib/modules/manager/pip-compile/extract.ts b/lib/modules/manager/pip-compile/extract.ts
index ed011867f7ad02..b3b8730c24f788 100644
--- a/lib/modules/manager/pip-compile/extract.ts
+++ b/lib/modules/manager/pip-compile/extract.ts
@@ -70,6 +70,7 @@ export async function extractAllPackageFiles(
   const lockFileArgs = new Map<string, PipCompileArgs>();
   const depsBetweenFiles: DependencyBetweenFiles[] = [];
   const packageFiles = new Map<string, PackageFile>();
+  const lockFileSources = new Map<string, PackageFile>();
   for (const fileMatch of fileMatches) {
     const fileContent = await readLocalFile(fileMatch, 'utf8');
     if (!fileContent) {
@@ -132,7 +133,9 @@ export async function extractAllPackageFiles(
         logger.debug(
           `pip-compile: ${packageFile} used in multiple output files`,
         );
-        packageFiles.get(packageFile)!.lockFiles!.push(fileMatch);
+        const existingPackageFile = packageFiles.get(packageFile)!;
+        existingPackageFile.lockFiles!.push(fileMatch);
+        lockFileSources.set(fileMatch, existingPackageFile);
         continue;
       }
       const content = await readLocalFile(packageFile, 'utf8');
@@ -180,11 +183,13 @@ export async function extractAllPackageFiles(
             );
           }
         }
-        packageFiles.set(packageFile, {
+        const newPackageFile: PackageFile = {
           ...packageFileContent,
           lockFiles: [fileMatch],
           packageFile,
-        });
+        };
+        packageFiles.set(packageFile, newPackageFile);
+        lockFileSources.set(fileMatch, newPackageFile);
       } else {
         logger.warn(
           { packageFile },
@@ -200,6 +205,25 @@ export async function extractAllPackageFiles(
     depsBetweenFiles,
     packageFiles,
   );
+
+  // This needs to go in reverse order to handle transitive dependencies
+  for (const packageFile of [...result].reverse()) {
+    for (const reqFile of packageFile.managerData?.requirementsFiles ?? []) {
+      let sourceFile: PackageFile | undefined = undefined;
+      if (fileMatches.includes(reqFile)) {
+        sourceFile = lockFileSources.get(reqFile);
+      } else if (packageFiles.has(reqFile)) {
+        sourceFile = packageFiles.get(reqFile);
+      }
+      if (!sourceFile) {
+        logger.warn(
+          `pip-compile: ${packageFile.packageFile} references ${reqFile} which does not appear to be a requirements file managed by pip-compile`,
+        );
+        continue;
+      }
+      sourceFile.lockFiles!.push(...packageFile.lockFiles!);
+    }
+  }
   logger.debug(
     'pip-compile: dependency graph:\n' +
       generateMermaidGraph(depsBetweenFiles, lockFileArgs),