In Central America, population and food demands are rising rapidly, while yields of staple crops, maize and beans, remain low. To identify the main factors limiting production, field trials were established in six maize- and bean-producing regions in Guatemala, Honduras and El Salvador, representing about three-quarters of the maize-producing area. Potential yield-limiting factors were evaluated in 2017 and included: water stress, nutrient deficiency, pest and disease pressure, and/or inter-plant competition. When considering all sites, improved fertilization and pest and disease control significantly improved yields in maize by 11 and 16%, respectively but did not have a significant effect in beans. Irrigation had no effect due to good rainfall distribution over the growing season. Optimized planting arrangement resulted in an average 18% increase in maize yield, making it the most promising factor evaluated. The treatment and site combinations that increased both crop productivity and net profit included management changes that improved resource use efficiency. However, the contribution of each limiting factor to yield gaps varied across sites and no treatment was effective at increasing yield consistently across sites. Production constraints are highly dependent on local management practices and agroecological location. Therefore, public and private development efforts that seek to increase production should conduct multi-year, participatory experiments to identify limitations pertinent to the area in question. The next step is then to evaluate sustainable and profitable practices, to address those limitations and provide sound recommendations to farmers while decreasing the environmental and economic costs.