In Indonesia, smallholder farmers play a crucial role in preserving biodiversity and cultural practices closely tied to food security. However, they face numerous sustainability challenges. Agroecology offers a promising approach to address these challenges by putting emphasis on earth’s carrying capacity and social equity. This study surveyed 442 smallholder farmers in different sub-districts of Malang and Lamongan provinces to assess their perceptions around agroecological principles. Using a 5-point Likert scale, the study captured and analyzed farmers’ perceptions and correlated these with their agricultural practices. Practices such as the overuse and underuse of fertilizers and imprudent pesticide applications were documented, while uncertainties in farmers’ capacity in adapting to unforeseen events were apparent. Despite limited awareness about biodiversity loss and soil degradation, many farmers believed in their potential to contribute to environmental restoration and most of them expressed satisfaction with their quality of life and income levels. Such insights were used to determine transition pathways towards more agroecological farming systems.