A fundamental challenge of land use management is to sustain the production of food, energy and fiber whilst preserving biodiversity and ecosystem functions. Some promising solutions to current resource-use conflicts are rooted in (agro) ecological intensification, which proposes that ecosystem functions provided by natural habitat can largely replace agrochemical inputs. Here, we evaluate how natural habitat is distributed in relation to agricultural input and the environmental potential for crop production, and whether natural habitat can explain the variations in yield not explained by management and environmental factors. In our analysis, we relied on environmental and management variables from 2858 soybean and 1548 individual maize fields provided by a farming organization in Argentina, and assessed landscape metrics of natural habitat composition (percentage of natural habitat) and configuration (edge density) for each one. We found that fields with higher fertilizer and seed input had lower percentages of natural habitat. Spatial variation in yield was well explained by environmental and management variables for both soybean and maize fields, and landscape metrics showed no relationship to the residuals of the models. However, fields recently transformed from natural habitat had higher yields than those with a long history of agricultural use. We conclude that compensatory management may mask the beneficial effects of natural habitat to some extent, especially in fields with intensive agrochemical use.