A method and system for dynamic and adaptive deployment of in-process agents to virtual machine based applications which may run on remote hosts is provided. A bootstrap agent is injected into the application, using standardized interfaces provided by virtual machine based systems like SUN MICROSYSTEMS' JAVA system or MICROSOFT's .NET system. The bootstrap agent establishes a network connection to a management server which provides binaries representing in-process agents in bytecode or native code format. The bootstrap agent sends data identifying its runtime environment to the management server, which determines the matching in-process agent binaries for the runtime environment of the connected agent and sends the selected binaries to the bootstrap agent. The bootstrap agent receives the binaries and installs them to its hosting virtual machine, according to their format (bytecode or native code).