Agricultural research deals with an extremely complex production system. Although a large variety of tools for the analysis of such systems have been developed, agricultural science has only been partially successful in providing solutions to farmers. Systems analysis often has been a synonym for quantitative, modeling exercises. Although these have led to a number of technological solutions for agricultural problems, the level of adoption of these solutions has been low because socioeconomic factors were lacking in the analysis. Farming systems approaches, on the other hand, included these socioeconomic conditions but failed to systematically apply the more technological tools. In this paper, we review the prototyping methodology that integrates participatory, socioeconomic approaches with a more technological approach. This prototyping methodology is composed of four major steps: (i) a thorough analysis of the farming system in close discussion with the farmer, (ii) the identification and execution of necessary biophysical and agronomic research, (iii) feedback of research results to the farmer and discussions on the implementation of the results, and (iv) the extension of the different solutions to other farms. This methodology has been applied for a Costa Rican banana (Musa spp.) plantation. Problems identified by the farmer were related to productivity, fertilization, and nematode control. Research made use of different approaches varying from monitoring of systems, analysis of problems related to productivity, experimentation to address fertility issues, and mechanistic simulation modeling for nematocide leaching. Research resulted in new prototypes of techniques to map banana yields, soil-specific fertilization, and nematode control.