To optimize the nutrient management of upland rice production on tropical ferralsols, a greenhouse experiment was established using the multi-nutrient omission approach. A reciprocal soil origin-rice cultivar transplant experiment was also conducted to better understand the relative contributions of the soil origin and the rice cultivar in rice nutrient limitation. We tested the deficiency of seven major and secondary nutrients [nitrogen (N), phosphorus (P), potassium (K), sulfur (S), calcium (Ca), magnesium (Mg), and silicon (Si)] and a solution of six micronutrients (B, Mn, Cu, Co, Na, Mo) likely to limit the growth of two upland rice cultivars, Chhomrong Dan and Nerica 4, on two Ferralsols from the highlands of Madagascar. We found severe multiple nutrient deficiencies. For both cultivars, P, Ca, N, Mg omission significantly depressed the shoot and root dry biomass and their amounts in plant tissues. However, the main limiting nutrients were not the same in both soils. We conclude that the multinutrient deficiencies observed for rice growth in the Ferralsols are site-specific, even though P limitation appears to be in common, and requires a holistic consideration of the mineral fertility, including micronutrients.