diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
index 4de1512..e8d8d26 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.js
@@ -7,10 +7,16 @@ export async function runPip(command, args) {
   try {
     const env = mergeSafeChainProxyEnvironmentVariables(process.env);
 
-    // Pass --cert with our CA to pip so it trusts our MITM for known registries.
-    // pip will append this to its default CA bundle, so it still validates
-    // non-registry HTTPS (GitHub, custom mirrors) against system CAs.
-    const finalArgs = [...args, "--cert", getCaCertPath()];
+    // If the user already provided --cert, respect their choice and do not override.
+    // Support both "--cert <path>" and "--cert=<path>" forms.
+    const hasUserCert = args.some((a, i) => {
+      if (a === "--cert") return true;
+      return typeof a === "string" && a.startsWith("--cert=");
+    });
+
+    // By default, pass --cert with our CA so pip trusts our MITM for known registries.
+    // Note: pip treats --cert as the CA bundle to use for TLS (it does not merge with system CAs).
+    const finalArgs = hasUserCert ? [...args] : [...args, "--cert", getCaCertPath()];
 
     const result = await safeSpawn(command, finalArgs, {
       stdio: "inherit",
diff --git a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
index 52a4148..f9ef43d 100644
--- a/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
+++ b/packages/safe-chain/src/packagemanager/pip/runPipCommand.spec.js
@@ -60,4 +60,28 @@ describe("runPipCommand --cert handling", () => {
     assert.strictEqual(capturedArgs.args[0], "install");
     assert.strictEqual(capturedArgs.args[1], "requests");
   });
+
+  it("should not override user-provided --cert <path>", async () => {
+    const res = await runPip("pip3", ["install", "requests", "--cert", "/tmp/user-ca.pem"]);
+    assert.strictEqual(res.status, 0);
+
+    // Ensure only the user-provided --cert is present
+    const certIndices = capturedArgs.args
+      .map((a, i) => (a === "--cert" ? i : -1))
+      .filter((i) => i >= 0);
+    assert.strictEqual(certIndices.length, 1, "should not inject an extra --cert");
+    const userPath = capturedArgs.args[certIndices[0] + 1];
+    assert.strictEqual(userPath, "/tmp/user-ca.pem", "should preserve user-provided cert path");
+  });
+
+  it("should not override user-provided --cert=<path>", async () => {
+    const res = await runPip("pip3", ["install", "requests", "--cert=/tmp/user-ca.pem"]);
+    assert.strictEqual(res.status, 0);
+
+    // Ensure args contain the inline --cert=<path> and no extra --cert token
+    const hasInline = capturedArgs.args.some((a) => typeof a === "string" && a.startsWith("--cert="));
+    assert.ok(hasInline, "should keep inline --cert=<path>");
+    const injectedIndex = capturedArgs.args.indexOf("--cert");
+    assert.strictEqual(injectedIndex, -1, "should not inject separate --cert when inline is provided");
+  });
 });
diff --git a/test/e2e/pip.e2e.spec.js b/test/e2e/pip.e2e.spec.js
index 7013121..05bdde9 100644
--- a/test/e2e/pip.e2e.spec.js
+++ b/test/e2e/pip.e2e.spec.js
@@ -193,4 +193,73 @@ describe("E2E: pip coverage", () => {
     );
   });
 
+  it(`pip3 can install from GitHub URL using system CAs`, async () => {
+    const shell = await container.openShell("zsh");
+    // Install a simple package from GitHub - this should use TCP tunnel, not MITM
+    // Using a popular, small package for testing
+    const result = await shell.runCommand('pip3 install --break-system-packages git+https://github.com/psf/requests.git@v2.32.3');
+
+    assert.ok(
+      result.output.includes("no malicious packages found."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+
+    // Verify installation succeeded (would fail if certificate validation broke)
+    assert.ok(
+      result.output.includes("Successfully installed") || result.output.includes("Requirement already satisfied"),
+      `Installation from GitHub failed - system CAs may not be working. Output was:\n${result.output}`
+    );
+
+    // Verify package was actually installed
+    const listResult = await shell.runCommand("pip3 list");
+    assert.ok(
+      listResult.output.includes("requests"),
+      `Package from GitHub was not installed. Output was:\n${listResult.output}`
+    );
+  });
+
+  it(`pip3 successfully validates certificates for HTTPS downloads`, async () => {
+    const shell = await container.openShell("zsh");
+    // Clear cache to force network download through proxy
+    await shell.runCommand("pip3 cache purge");
+
+    const result = await shell.runCommand('pip3 install --break-system-packages certifi');
+
+    assert.ok(
+      result.output.includes("no malicious packages found."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+
+    // Verify successful installation (would fail with SSL/certificate errors if --cert wasn't working)
+    assert.ok(
+      result.output.includes("Successfully installed"),
+      `Installation should succeed with proper certificate validation. Output was:\n${result.output}`
+    );
+
+    // Should NOT contain SSL or certificate errors
+    assert.ok(
+      !result.output.match(/SSL|certificate verify failed|CERTIFICATE_VERIFY_FAILED/i),
+      `Should not have SSL/certificate errors. Output was:\n${result.output}`
+    );
+  });
+
+  it(`pip3 handles external HTTPS correctly (e.g., downloading from CDN)`, async () => {
+    const shell = await container.openShell("zsh");
+    // Test installing from a direct HTTPS URL (not a registry)
+    // This validates that non-registry HTTPS traffic works with system CAs
+    const result = await shell.runCommand('pip3 install --break-system-packages https://files.pythonhosted.org/packages/70/8e/0e2d847013cb52cd35b38c009bb167a1a26b2ce6cd6965bf26b47bc0bf44/requests-2.31.0-py3-none-any.whl');
+
+    assert.ok(
+      result.output.includes("no malicious packages found."),
+      `Output did not include expected text. Output was:\n${result.output}`
+    );
+
+    // Since this is from pythonhosted.org, it should be MITM'd by safe-chain
+    // But the certificate validation should still work
+    assert.ok(
+      result.output.includes("Successfully installed") || result.output.includes("Requirement already satisfied"),
+      `Installation from direct HTTPS URL failed. Output was:\n${result.output}`
+    );
+  });
+
 });