Few longitudinal studies link agricultural biodiversity, land use and food access in rural landscapes. In this paper, we test the hypothesis that, in a context of economic change, cash crop expansion is associated with deforestation, reduced agrobiodiversity and changes in food access. For this purpose, we analysed data collected from the same 53 upland and floodplain mestizo households in Ucayali, Peru, in 2000 and 2015. We found an emerging transition towards less diversified food access coupled with loss of forest cover and reduced agricultural biodiversity. In 2015, diets appeared to rely on fewer food groups, fewer food items, and on products increasingly purchased in the market compared to 2000. Wild fruits and plants were mentioned, but rarely consumed. Agricultural production systems became more specialised with a shift towards commercial crops. Peak deforestation years in the 15-year period appeared linked with incentives for agricultural expansion. Our results suggest an overall trend from diversified productive and “extractive” systems and more diverse food access, towards specialized productive systems, with less diverse food access and stronger market orientation (both in production and consumption). The assumption in the food and agricultural sciences that increased income and market-orientation is linked to improved food security, is challenged by our integrated analyses of food access, agrobiodiversity, land use and forest cover. Our results highlight the importance of longitudinal, multidimensional, systemic analyses, with major implications for land use, food and health policies. The potential risks of parallel homogenisation of diets and agricultural production systems require interdisciplinary research and policies that promote integrated landscape approaches for sustainable and inclusive food systems.