Powdery mildew and tomato spotted wilt virus (TSWV) are the two main threats to pepper plants (Capsicum annuum) grown in greenhouses causing severe damage and yield loss. The paper reports the development of a robotic disease monitoring system for early detection of both threats. The research faced several challenges as, currently, algorithms for powdery mildew detection have only been implemented on other crops and there are no known algorithms for TSWV detection. Moreover, monitoring several diseases of pepper plants using a single monitoring system has not been reported. The system development was based on a holistic approach, integrating the design of both motion and perception systems. Preliminary results for TSWV detection are promising. Analysis of powdery mildew database is currently being conducted. The physical hardware system has been constructed and once the image processing algorithms are finalized, the system will be ready for extensive testing.