diff --git a/.gitignore b/.gitignore
index 1b32046..611b278 100644
--- a/.gitignore
+++ b/.gitignore
@@ -11,3 +11,4 @@ Cargo.lock
 /reproducible/binaries.sha256sum
 /reproducible/elf2tab.txt
 /reproducible/reproduced.tar
+__pycache__
diff --git a/deploy.py b/deploy.py
index 42579a2..b3daa6f 100755
--- a/deploy.py
+++ b/deploy.py
@@ -710,6 +710,22 @@ class OpenSKInstaller:
             check=False,
             timeout=None,
         ).returncode
+
+    # Configure OpenSK through vendor specific command if needed
+    if any([
+        self.args.lock_device,
+        self.args.config_cert,
+        self.args.config_pkey,
+    ]):
+      # pylint: disable=g-import-not-at-top,import-outside-toplevel
+      import tools.configure
+      tools.configure.main(
+          argparse.Namespace(
+              batch=False,
+              certificate=self.args.config_cert,
+              priv_key=self.args.config_pkey,
+              lock=self.args.lock_device,
+          ))
     return 0
 
 
@@ -770,6 +786,33 @@ if __name__ == "__main__":
       help=("Erases the persistent storage when installing an application. "
             "All stored data will be permanently lost."),
   )
+  main_parser.add_argument(
+      "--lock-device",
+      action="store_true",
+      default=False,
+      dest="lock_device",
+      help=("Try to disable JTAG at the end of the operations. This "
+            "operation may fail if the device is already locked or if "
+            "the certificate/private key are not programmed."),
+  )
+  main_parser.add_argument(
+      "--inject-certificate",
+      default=None,
+      metavar="PEM_FILE",
+      type=argparse.FileType("rb"),
+      dest="config_cert",
+      help=("If this option is set, the corresponding certificate "
+            "will be programmed into the key as the last operation."),
+  )
+  main_parser.add_argument(
+      "--inject-private-key",
+      default=None,
+      metavar="PEM_FILE",
+      type=argparse.FileType("rb"),
+      dest="config_pkey",
+      help=("If this option is set, the corresponding private key "
+            "will be programmed into the key as the last operation."),
+  )
   main_parser.add_argument(
       "--programmer",
       metavar="METHOD",
diff --git a/setup.sh b/setup.sh
index 903e0e3..13ad9b0 100755
--- a/setup.sh
+++ b/setup.sh
@@ -44,3 +44,6 @@ rustup target add thumbv7em-none-eabi
 # Install dependency to create applications.
 mkdir -p elf2tab
 cargo install elf2tab --version 0.6.0 --root elf2tab/
+
+# Install python dependencies to factory configure OpenSK (crypto, JTAG lockdown)
+pip3 install --user --upgrade colorama tqdm cryptography fido2
diff --git a/tools/configure.py b/tools/configure.py
new file mode 100755
index 0000000..eff1166
--- /dev/null
+++ b/tools/configure.py
@@ -0,0 +1,197 @@
+#!/usr/bin/env python3
+# Copyright 2020 Google LLC
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# Lint as: python3
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+
+import argparse
+import getpass
+import datetime
+import sys
+import uuid
+
+import colorama
+from tqdm.auto import tqdm
+
+from cryptography import x509
+from cryptography.hazmat.primitives import serialization
+from cryptography.hazmat.primitives.asymmetric import ec
+
+from fido2 import ctap
+from fido2 import ctap2
+from fido2 import hid
+
+OPENSK_VID_PID = (0x1915, 0x521F)
+OPENSK_VENDOR_CONFIGURE = 0x40
+
+
+def fatal(msg):
+  tqdm.write("{style_begin}fatal:{style_end} {message}".format(
+      style_begin=colorama.Fore.RED + colorama.Style.BRIGHT,
+      style_end=colorama.Style.RESET_ALL,
+      message=msg))
+  sys.exit(1)
+
+
+def error(msg):
+  tqdm.write("{style_begin}error:{style_end} {message}".format(
+      style_begin=colorama.Fore.RED,
+      style_end=colorama.Style.RESET_ALL,
+      message=msg))
+
+
+def info(msg):
+  tqdm.write("{style_begin}info:{style_end} {message}".format(
+      style_begin=colorama.Fore.GREEN + colorama.Style.BRIGHT,
+      style_end=colorama.Style.RESET_ALL,
+      message=msg))
+
+
+def get_opensk_devices(batch_mode):
+  devices = []
+  for dev in hid.CtapHidDevice.list_devices():
+    if (dev.descriptor["vendor_id"],
+        dev.descriptor["product_id"]) == OPENSK_VID_PID:
+      if dev.capabilities & hid.CAPABILITY.CBOR:
+        if batch_mode:
+          devices.append(ctap2.CTAP2(dev))
+        else:
+          return [ctap2.CTAP2(dev)]
+  return devices
+
+
+def get_private_key(data, password=None):
+  # First we try without password
+  try:
+    return serialization.load_pem_private_key(data, password=None)
+  except TypeError:
+    # Maybe we need a password then
+    if sys.stdin.isatty():
+      password = getpass.getpass(prompt="Private key password: ")
+    else:
+      password = sys.stdin.readline().rstrip()
+    return get_private_key(data, password=password.encode(sys.stdin.encoding))
+
+
+def main(args):
+  colorama.init()
+  # We need either both the certificate and the key or none
+  if bool(args.priv_key) ^ bool(args.certificate):
+    fatal("Certificate and private key must be set together or both omitted.")
+
+  cbor_data = {1: args.lock}
+
+  if args.priv_key:
+    cbor_data[1] = args.lock
+    priv_key = get_private_key(args.priv_key.read())
+    if not isinstance(priv_key, ec.EllipticCurvePrivateKey):
+      fatal("Private key must be an Elliptic Curve one.")
+    if not isinstance(priv_key.curve, ec.SECP256R1):
+      fatal("Private key must use Secp256r1 curve.")
+    if priv_key.key_size != 256:
+      fatal("Private key must be 256 bits long.")
+    info("Private key is valid.")
+
+    cert = x509.load_pem_x509_certificate(args.certificate.read())
+    # Some sanity/validity checks
+    now = datetime.datetime.now()
+    if cert.not_valid_before > now:
+      fatal("Certificate validity starts in the future.")
+    if cert.not_valid_after <= now:
+      fatal("Certificate expired.")
+    pub_key = cert.public_key()
+    if not isinstance(pub_key, ec.EllipticCurvePublicKey):
+      fatal("Certificate public key must be an Elliptic Curve one.")
+    if not isinstance(pub_key.curve, ec.SECP256R1):
+      fatal("Certificate public key must use Secp256r1 curve.")
+    if pub_key.key_size != 256:
+      fatal("Certificate public key must be 256 bits long.")
+    if pub_key.public_numbers() != priv_key.public_key().public_numbers():
+      fatal("Certificate public doesn't match with the private key.")
+    info("Certificate is valid.")
+
+    cbor_data[2] = {
+        1:
+            cert.public_bytes(serialization.Encoding.DER),
+        2:
+            priv_key.private_numbers().private_value.to_bytes(
+                length=32, byteorder='big', signed=False)
+    }
+
+  for authenticator in tqdm(get_opensk_devices(args.batch)):
+    # If the device supports it, wink to show which device
+    # we're going to program
+    if authenticator.device.capabilities & hid.CAPABILITY.WINK:
+      authenticator.device.wink()
+    aaguid = uuid.UUID(bytes=authenticator.get_info().aaguid)
+    info(("Programming device {} AAGUID {} ({}). "
+          "Please touch the device to confirm...").format(
+              authenticator.device.descriptor.get("product_string", "Unknown"),
+              aaguid, authenticator.device))
+    try:
+      result = authenticator.send_cbor(
+          OPENSK_VENDOR_CONFIGURE,
+          data=cbor_data,
+      )
+      info("Certificate: {}".format("Present" if result[1] else "Missing"))
+      info("Private Key: {}".format("Present" if result[2] else "Missing"))
+      if result[3]:
+        info("Device locked down!")
+    except ctap.CtapError as ex:
+      if ex.code.value == ctap.CtapError.ERR.INVALID_COMMAND:
+        error("Failed to configure OpenSK (unsupported command).")
+
+
+if __name__ == "__main__":
+  parser = argparse.ArgumentParser()
+  parser.add_argument(
+      "--batch",
+      default=False,
+      action="store_true",
+      help=(
+          "When batch processing is used, all plugged OpenSK devices will "
+          "be programmed the same way. Otherwise (default) only the first seen "
+          "device will be programmed."),
+  )
+  parser.add_argument(
+      "--certificate",
+      type=argparse.FileType("rb"),
+      default=None,
+      metavar="PEM_FILE",
+      dest="certificate",
+      help=("PEM file containing the certificate to inject into "
+            "OpenSK authenticator."),
+  )
+  parser.add_argument(
+      "--private-key",
+      type=argparse.FileType("rb"),
+      default=None,
+      metavar="PEM_FILE",
+      dest="priv_key",
+      help=("PEM file containing the private key associated "
+            "with the certificate."),
+  )
+  parser.add_argument(
+      "--lock-device",
+      default=False,
+      action="store_true",
+      dest="lock",
+      help=("Locks the device (i.e. bootloader and JTAG access). "
+            "This command can fail if the certificate or the private key "
+            "haven't been both programmed yet."),
+  )
+  main(parser.parse_args())