diff --git a/letsencrypt-auto-source/letsencrypt-auto b/letsencrypt-auto-source/letsencrypt-auto
index 9c8ccf344..b5cac23e6 100755
--- a/letsencrypt-auto-source/letsencrypt-auto
+++ b/letsencrypt-auto-source/letsencrypt-auto
@@ -761,13 +761,8 @@ BootstrapMageiaCommon() {
 # Set Bootstrap to the function that installs OS dependencies on this system
 # and BOOTSTRAP_VERSION to the unique identifier for the current version of
 # that function. If Bootstrap is set to a function that doesn't install any
-# packages (either because --no-bootstrap was included on the command line or
-# we don't know how to bootstrap on this system), BOOTSTRAP_VERSION is not set.
-if [ "$NO_BOOTSTRAP" = 1 ]; then
-  Bootstrap() {
-    :
-  }
-elif [ -f /etc/debian_version ]; then
+# packages BOOTSTRAP_VERSION is not set.
+if [ -f /etc/debian_version ]; then
   Bootstrap() {
     BootstrapMessage "Debian-based OSes"
     BootstrapDebCommon
@@ -863,6 +858,17 @@ else
   }
 fi
 
+# We handle this case after determining the normal bootstrap version to allow
+# variables like USE_PYTHON_3 to be properly set. As described above, if the
+# Bootstrap function doesn't install any packages, BOOTSTRAP_VERSION should not
+# be set so we unset it here.
+if [ "$NO_BOOTSTRAP" = 1 ]; then
+  Bootstrap() {
+    :
+  }
+  unset BOOTSTRAP_VERSION
+fi
+
 # Sets PREV_BOOTSTRAP_VERSION to the identifier for the bootstrap script used
 # to install OS dependencies on this system. PREV_BOOTSTRAP_VERSION isn't set
 # if it is unknown how OS dependencies were installed on this system.
diff --git a/letsencrypt-auto-source/letsencrypt-auto.template b/letsencrypt-auto-source/letsencrypt-auto.template
index 96e5c2db0..2ce337002 100755
--- a/letsencrypt-auto-source/letsencrypt-auto.template
+++ b/letsencrypt-auto-source/letsencrypt-auto.template
@@ -300,13 +300,8 @@ DeterminePythonVersion() {
 # Set Bootstrap to the function that installs OS dependencies on this system
 # and BOOTSTRAP_VERSION to the unique identifier for the current version of
 # that function. If Bootstrap is set to a function that doesn't install any
-# packages (either because --no-bootstrap was included on the command line or
-# we don't know how to bootstrap on this system), BOOTSTRAP_VERSION is not set.
-if [ "$NO_BOOTSTRAP" = 1 ]; then
-  Bootstrap() {
-    :
-  }
-elif [ -f /etc/debian_version ]; then
+# packages BOOTSTRAP_VERSION is not set.
+if [ -f /etc/debian_version ]; then
   Bootstrap() {
     BootstrapMessage "Debian-based OSes"
     BootstrapDebCommon
@@ -402,6 +397,17 @@ else
   }
 fi
 
+# We handle this case after determining the normal bootstrap version to allow
+# variables like USE_PYTHON_3 to be properly set. As described above, if the
+# Bootstrap function doesn't install any packages, BOOTSTRAP_VERSION should not
+# be set so we unset it here.
+if [ "$NO_BOOTSTRAP" = 1 ]; then
+  Bootstrap() {
+    :
+  }
+  unset BOOTSTRAP_VERSION
+fi
+
 # Sets PREV_BOOTSTRAP_VERSION to the identifier for the bootstrap script used
 # to install OS dependencies on this system. PREV_BOOTSTRAP_VERSION isn't set
 # if it is unknown how OS dependencies were installed on this system.
diff --git a/letsencrypt-auto-source/tests/centos6_tests.sh b/letsencrypt-auto-source/tests/centos6_tests.sh
index a0e96edf8..2c6dcf734 100644
--- a/letsencrypt-auto-source/tests/centos6_tests.sh
+++ b/letsencrypt-auto-source/tests/centos6_tests.sh
@@ -69,5 +69,13 @@ fi
 echo "PASSED: Successfully upgraded to Python3 when only Python2.6 is present."
 echo ""
 
+export VENV_PATH=$(mktemp -d)
+"$LE_AUTO" -n --no-bootstrap --no-self-upgrade --version >/dev/null 2>&1
+if [ "$($VENV_PATH/bin/python -V 2>&1 | cut -d" " -f2 | cut -d. -f1)" != 3 ]; then
+  echo "Python 3 wasn't used with --no-bootstrap!"
+  exit 1
+fi
+unset VENV_PATH
+
 # test using python3
 pytest -v -s certbot/letsencrypt-auto-source/tests