Remotely configuring an online computer system. A configuration file is generated at a management controller associated with a computer system in response to a request from a configuration utility associated with a user device, wherein the user device is located remotely from the computer system. The configuration file is sent from the management controller to the configuration utility via a network connection. A modified configuration file is received at the management controller from the configuration utility via the network connection, wherein the modified configuration file comprises system level changes to a configuration of the computer system. The system level changes from the modified configuration file are implemented at the computer system while an operating system associated with the computer system is online.