A system and method is presented that installs an agent on a computer system that monitors the start of processes by the computer system and that identifies the start of processes that perform container management activities, like starting and stopping container environments. On start of a container manager process, the agent starts a container manager agent that establishes a monitoring connection to the container manager process. The container manager agent monitors activities performed by the container manager process to detect the start of new container environments by the container manager process. On detection of a container start, the container manager agent manipulates the container configuration in a way that a process type specific in-process agent is automatically injected into processes started inside the container.