This study sought to examine the factors influencing smallholder farmers’ participation in the fertilizer subsidy scheme in Nigeria and estimate the impact of the scheme on farmers’ productivity, food security and nutrition outcomes. One of the key findings of the study is that the subsidy scheme had significant impact on farmers’ productivity. We found that subsidy significantly increases productivity among the subsidized farmers; and that the subsidized farmers would have had higher productivity than their non-subsidized counterparts had the non-subsidized farmers participated in the subsidy scheme. The study also revealed that without subsidy productivity is significantly lower among non-subsidized farmers; and they would have had lower productivity than subsidized farmers in a situation where the subsidized farmers had not participated in the subsidy scheme. Evidently, on the average, the results show that subsidized farmers have higher productivity potential than non-subsidized farmers. Another remarkable finding is in respect of food security and nutrition. We found that the subsidy scheme had significant impact on food security of the smallholder farmers. Specifically, the participants are found to be better off participating than not participating. Moreover, the results show that it would have been possible for the non-participants to increase their food security if they had participated in the subsidy scheme. The results in respect of the two nutrition outcomes considered are mixed. As regards mineral intake adequacy we found positive treatment effect on the treated and negative effect on the untreated. For vitamin intake adequacy the subsidy impact is positive.