diff --git a/installation_and_upgrade/ibex_install_utils/install_tasks.py b/installation_and_upgrade/ibex_install_utils/install_tasks.py
index 47de75d..8d3a300 100644
--- a/installation_and_upgrade/ibex_install_utils/install_tasks.py
+++ b/installation_and_upgrade/ibex_install_utils/install_tasks.py
@@ -276,7 +276,12 @@ def run_vhd_creation(self):
             self._mysql_tasks.install_mysql_for_vhd()
             self._client_tasks.install_ibex_client()
             self._server_tasks.setup_config_repository()
-            self._server_tasks.upgrade_instrument_configuration()
+
+            # Some config upgrade steps require MySQL to be running
+            # For the VHD build, we can always assume we have a MYSQL_PASSWORD env variable
+            with self._mysql_tasks.temporarily_run_mysql(os.getenv("MYSQL_PASSWORD")):
+                self._server_tasks.upgrade_instrument_configuration()
+
             self._server_tasks.setup_calibrations_repository()
             self._server_tasks.update_calibrations_repository()
             self._vhd_tasks.initialize_var_dir()
diff --git a/installation_and_upgrade/ibex_install_utils/tasks/mysql_tasks.py b/installation_and_upgrade/ibex_install_utils/tasks/mysql_tasks.py
index 8cf6d96..31bfb48 100644
--- a/installation_and_upgrade/ibex_install_utils/tasks/mysql_tasks.py
+++ b/installation_and_upgrade/ibex_install_utils/tasks/mysql_tasks.py
@@ -1,3 +1,4 @@
+import contextlib
 import os
 import shutil
 import subprocess
@@ -159,45 +160,18 @@ def _initialize_mysql_data_area_for_vhd(self):
             ]
         ).run()
 
-    def _setup_database_users_and_tables(self, vhd_install=True):
+    @contextlib.contextmanager
+    def temporarily_run_mysql(self, sql_password: str):
         mysqld = os.path.join(MYSQL8_INSTALL_DIR, "bin", "mysqld.exe")
 
-        sql_password = self.prompt.prompt("Enter the MySQL root password:", UserPrompt.ANY,
-                                          os.getenv("MYSQL_PASSWORD", "environment variable not set"),
-                                          show_automatic_answer=False)
-
-        if vhd_install:  # Service won't have been started yet
-            # spawn service in background
-            subprocess.Popen(mysqld, creationflags=DETACHED_PROCESS)
+        # spawn service in background
+        subprocess.Popen(mysqld, creationflags=DETACHED_PROCESS)
 
-            sleep(5)  # Chance for the service to spawn
+        sleep(5)  # Chance for the service to spawn
 
-        RunProcess(
-            executable_directory=os.path.join(MYSQL8_INSTALL_DIR, "bin"),
-            working_dir=os.path.join(MYSQL8_INSTALL_DIR, "bin"),
-            executable_file="mysql.exe",
-            prog_args=[
-                '-u',
-                'root',
-                '-e',
-                f'ALTER USER \'root\'@\'localhost\' IDENTIFIED WITH mysql_native_password BY \'{sql_password}\';FLUSH '
-                f'privileges; '
-                    ,
-
-            ],
-            log_command_args=False,  # To make sure password doesn't appear in jenkins log.
-        ).run()
-
-        RunProcess(
-            working_dir=SYSTEM_SETUP_PATH,
-            executable_directory=SYSTEM_SETUP_PATH,
-            executable_file="config_mysql.bat",
-            prog_args=[sql_password],
-            log_command_args=False,  # To make sure password doesn't appear in jenkins log.
-        ).run()
-
-        if vhd_install:
-            # For VHD install only, stop mysql when done
+        try:
+            yield
+        finally:
             RunProcess(
                 executable_directory=os.path.join(MYSQL8_INSTALL_DIR, "bin"),
                 working_dir=os.path.join(MYSQL8_INSTALL_DIR, "bin"),
@@ -211,6 +185,43 @@ def _setup_database_users_and_tables(self, vhd_install=True):
                 log_command_args=False,  # To make sure password doesn't appear in jenkins log.
             ).run()
 
+    def _setup_database_users_and_tables(self, vhd_install=True):
+        sql_password = self.prompt.prompt("Enter the MySQL root password:", UserPrompt.ANY,
+                                          os.getenv("MYSQL_PASSWORD", "environment variable not set"),
+                                          show_automatic_answer=False)
+
+        if vhd_install:
+            # In the VHD install, need to explicitly temporarily run MySQL.
+            cm = self.temporarily_run_mysql(sql_password)
+        else:
+            # In normal installs, MySQL is already running as a service so do nothing
+            cm = contextlib.nullcontext()
+
+        with cm:
+            RunProcess(
+                executable_directory=os.path.join(MYSQL8_INSTALL_DIR, "bin"),
+                working_dir=os.path.join(MYSQL8_INSTALL_DIR, "bin"),
+                executable_file="mysql.exe",
+                prog_args=[
+                    '-u',
+                    'root',
+                    '-e',
+                    f'ALTER USER \'root\'@\'localhost\' IDENTIFIED WITH mysql_native_password BY \'{sql_password}\';FLUSH '
+                    f'privileges; '
+                        ,
+
+                ],
+                log_command_args=False,  # To make sure password doesn't appear in jenkins log.
+            ).run()
+
+            RunProcess(
+                working_dir=SYSTEM_SETUP_PATH,
+                executable_directory=SYSTEM_SETUP_PATH,
+                executable_file="config_mysql.bat",
+                prog_args=[sql_password],
+                log_command_args=False,  # To make sure password doesn't appear in jenkins log.
+            ).run()
+
     def _setup_mysql8_service(self):
         mysqld = os.path.join(MYSQL8_INSTALL_DIR, "bin", "mysqld.exe")
         admin_commands = AdminCommandBuilder()