Remote Amazonian communities are often largely self-sufficient, made possible in part by their agricultural skills and deep ecological knowledge of their landscapes. Mastery of their local flora undoubtedly plays a vital role in daily life, yet communities in the Amazon can vary widely in both the diversity of plants that they utilize and in how they manage plants in their agricultural landholdings. The dominant drivers of these differences in ecological knowledge and practices between communities are not clearly understood. We compare the agricultural practices and diversity of utilized plants in an Indigenous Urarina community and a Mestizo community in the Peruvian Amazon. Through field surveys and farmer interviews, we assessed the diversity of utilized plants found in the homegardens (N = 17) and chacras (cropped fields; N = 47), as well as multiple agricultural characteristics of the chacras and fallow fields (N = 32). Households from the Mestizo community cultivated a larger land area, while both communities utilized relatively short fallow times of < 6 years. Across both communities, farmers make use of a total of 207 plant species belonging to 60 plant families for various resources, including food, spices, medicine, fuel, craft, construction, hunting/fishing, and spiritual/cultural uses. Species diversity of utilized plants was significantly higher in the Urarina community, likely reflecting their longer historical roots in the region, lower reliance on a market economy, greater reliance on farm and forest products, and higher degree of biocultural relationship to the land. Kin size was negatively correlated with homegarden diversity, while increasing household wealth led to more species diversity in Urarina landholdings, but less diversity in Mestizo landholdings. These results suggest that both Mestizo and Indigenous communities, and especially the latter, play an important role in the conservation of traditional ecological knowledge and agrobiodiversity in the Peruvian Amazon; however, increasing market integration may jeopardize the biocultural relationships that undergird this in situ conservation.