The Malian Government has introduced the Fertilizer Subsidy Program as a policy strategy to increase agricultural productivity and food production with the aim of improving the food security and well-being of smallholder farm households. However, there is a lack of reliable evidence regarding the effects of the subsidy program. We tested the effects of fertilizer subsidies on diet quality of women of reproductive age by applying propensity score matching methods to farm household survey data collected in 2018. We found that subsidized fertilizer has a positive effect on overall women’s dietary diversity in the Niger Delta but is negatively associated with the overall dietary diversity in the Koutiala Plateau. One of the innovations of this study is that the dietary diversity score is broken down according to food supply sources. Analysis by component allows a thorough understanding of the channel through which the subsidized fertilizer program affects women's nutrition outcomes. A close look at the different components of women's dietary diversity reveals no effects on dietary diversity from the consumption of own production in either of the two zones. Analysis showed a negative impact of subsidized fertilizer on dietary diversity sourced from gift food in Niger Delta. Finally, we found that the effect of subsidized fertilizer on the dietary diversity sourced from purchased food was strong and positive in the Niger Delta, but negative in the Koutiala Plateau. The negative results for the Koutiala Plateau are not entirely surprising given the history of the “Sikasso Paradox.” Decomposing diet diversity by food source suggests that income is the main pathway linking subsidized fertilizers program to women’s nutrition outcomes.