A fundamental shift to a total system approach for crop management in greenhouses is urgently needed to resolve escalating economic and environmental consequences of long-lasting undesired effects of synthetic pesticides used in combating agricultural pests. The aim of this study was to examine a potential new approach i.e. Microbial-based Production System (MPS) for greenhouse-grown peppers. For this purpose, a two-year experiment in greenhouse was carried out in southwestern Turkey (Antalya) in 2011 and 2012, and only microbial-based products were used to suppress and control invertebrate pests (insects, mites, nematodes, gastropods, etc.) and diseases. In addition, biostimulants, inoculants, and bioyield enhancers were used for plant growth, being supported with three macro elements (NPK: Nitrogen-Phosphorus-Potassium) that are considered to be essential elements for plant growth and development. A conventional plot, largely based on the use of synthetic chemical inputs, such as fertilizers and pesticides, was included as the control. The efficacy of the MPS was evaluated by monitoring the population development of the key arthropod pests, such as the cotton whitefly Bemisia tabaci (Gennadius) (Homoptera: Aleyrodidae), the western flower thrips Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) etc. and their natural enemies compared with that in a Conventional Production System (CPS). The results showed significantly lower numbers of the key pests, but higher numbers of natural enemies were seen in the MPS of greenhouse-grown peppers compared with the CPS throughout the study. Total yield was relatively higher in the CPS than the MPS in both experimental years.