Conserving crop diversity is promoted for global food system stability and creating local benefits like improved farmer nutrition, incomes and adaptive capacities. However, little is known about how farmers make decisions shaping crop diversity, and how conservation efforts can be aligned with farmers’ goals. This study examines how interacting values, rules and knowledge shape decisions of subsistence farmers in central India. Findings suggest that farmers’ values play a central role in shaping crop diversity. Their culinary and health preferences for consuming various self-cultivated crops primarily drive portfolio decisions. Farmers are hesitant to invest in commercial agricultural because of unreliable returns. Furthermore, they prefer to control water availability and land quality as means of coping with environmental change, rather than resorting to crop diversification. Finally, a rich understanding of local crop diversity dynamics questions the ethics of expecting marginal farmers to shoulder the burden of conservation for global gain, suggesting ex-situ strategies are appropriate where in-situ practices are not autonomously selected. Overall, the analysis demonstrates the importance of understanding farmer-level decision-making for wider crop diversity conservation debates.