Business processes are often likely to undergo drastic changes and hence the workflow systems that model, simulate and enact these processes should support the monitoring and controlling of processes. In extension to our previous work on the framework for an adaptive and distributed agent based workflow system JBees, this paper describes the agents that are embedded to our system, that can monitor and control the system based upon the data obtained through simulation. In the monitoring part we focus on the performance indicators such as occupation rate, throughput time and average waiting time of various processes and tasks. We also compare the efficiency of various resources for the similar tasks. The controlling agent continuously looks for the anomalies against the criteria defined by the human manager/user with the data obtained from the system and informs the management agent to initiate appropriate action.