Overall, Integrated Pest Management (IPM) is considered a success story within Controlled Environment Agriculture (CEA) systems but this assertion is strongly dependant on technology levels and crop plant species. The estimated percentage under biological and integrated control in CEA in 2007 was 5% of the total world greenhouse area. In spite of substantial advances, IPM mostly concerns popular vegetables and sophisticated greenhouses, suggesting that biological control used without the help of physical control, e. g. screen-barriers and climate management, and multi-pest resistant varieties is a major challenge to overcome. Up to now, biological control has been implemented empirically at the cost of huge experimental efforts in order to provide wide-test ranges of biological control agents (BCAs) and that, by the same token, counterbalance numerous unexplained failures at the crop level. Satisfactory answers to pest problems require a shift in understanding, such as promoting biological agents as well as more widely ecologically-sound practices. Despite being poorly biodiversified, many complex interactions can occur between biotic components in agro-ecosystems such as CEA. Understanding these interactions is a major hurdle to overcome for the development of future IPM strategies. The ecological approach, based on both theoretical and applied studies, is of major interest to describe the biotic interactions taking place between the crop, pests and BCAs, as well as to refine pest control methods, for example, through the use of multiple natural enemies. Such an approach can highlight crucial information to choose BCA species accurately with respect to their intra-specific characteristics, i.e. functional and numerical responses, and inter-specific interactions. It may also assist the design of robust, efficient and complementary BCA associations targeted to multipest control issues. Experimental evidence of unexpected pest/pest, pest/BCAs, BCAs/BCAs interactions observed on tomato and rose crops, and their respective impact on IPM, are presented.