Agricultural extension requires close communication with farmers, and researchers must consider farmers’ perspectives on crop management. Farmers tend to take into account the canopy appearance when they decide on fertilizer application, and this is often neglected in crop management recommendations by researchers. Our objectives were to dissect the growth characteristics that farmers implicitly account for in nutrient management of tropical rice. Farmer participatory trials were conducted in irrigated and rainfed lowlands in the Philippines during the wet seasons of 2014, 2015, and 2016. Each year, 30 participating farmers made decisions on fertilizer management for plots with different seedling ages and planting densities. These treatments greatly changed the canopy appearance, and affected farmer decisions on nitrogen (N) management, particularly in the first year. We found that plant height and leaf greenness were the major determinants of their decisions in irrigated lowlands. Under rainfed conditions, the risk of drought made farmers focus on tillering rather than plant elongation and leaf color during early growth stages, and on canopy cover and plant elongation during later stages. Across years and water regimes, farmers applied 78% more N than researchers without generally increasing grain yield. Since crop diagnosis is a key for successful management by farmers, guidelines for efficient nutrient management should include numerical targets for the traits emphasized by farmers. That will help farmers better understand their crops, and the guidelines will be more user-friendly than providing only a fertilizer application prescription.