Methods, systems, and apparatus, including computer programs encoded on computer storage media, for dynamically injecting secrets in a pipeline integration system. One of the methods includes receiving, by a pipeline controller, a job identifying a pipeline for executing a plurality of tasks. A preparatory task is invoked for the pipeline that obtains one or more original task definitions for the identified pipeline and generates one or more modified task definitions for the pipeline, wherein each modified task definition references one or more variablized secret names specified as the value of the reserved variable of the one or more configuration files. One or more subsequent execution tasks are invoked using each respective modified task definition. One or more retrieved secrets are injected into an execution environment for each particular execution task.