Provided are a computer program product, system, and method for generating and deploying code files compiled on build machines. Source code is maintained at a deployment system. Commands are sent to build machines to compile the source code into object code. The build machines have different operating systems to compile the object code. The deployment system stores the object code for each build machine in an object code file directory to provide executable object code for an operating system installed at the build machine. Different object code file directories are maintained for the object code compiled by the build machines having different operating systems. Access is provided to the object code in the object code file directories to run-time machines. Each run-time machine accesses the object code file directory in the deployment system having the object code compiled for an operating system version deployed on the run-time machine.