A system and method for creating and supporting multiple customized versions of a software application within a web-based environment is disclosed. Customized code is created for a user of the software application. This code is invoked by inserting code hooks such as subroutine calls into the software application. The file containing the customized code is moved to a respective physical directory created for the user. An association is then created between this physical directory and a virtual directory of the type supported by IIS and other similar web servers. Finally, the virtual directory and the customized code file are identified by a reference provided with the software application. When a run-time version of the code is generated for the user, this reference along with the association created between the virtual and physical directories result in generation of a user-specific version of the software application.