Many sub-Saharan African countries implementing agricultural input subsidies programmes (AISP) concentrate on fertilizers and staple food crops which may have little or no effect on consumption of diverse nutrient dense non-staple foods. The programme in Malawi – the Farm Input Subsidy Programme (FISP) – includes legume seeds, but little research has been undertaken to evaluate the effects of this strategy on household dietary diversity. In this study, we used two waves of integrated household panel survey data of 2013 and 2016 to examine the dietary diversity gains from inclusion of legume seed coupons in the programme. The control function approach for dealing with selection bias into a programme is used in Poisson regression of panel data. The results show that access as well as redemption of legume coupons is positively associated with diversified diets. This is especially through location fixed effects in the southern region of Malawi, higher production diversity, greater land holding sizes and the sale of maize. Further, households that had less need to satisfy hunger through the growing of maize were those likely to redeem legume coupons. The results suggest a more nuanced pathway of impact from coupon access, redemption or type of crop produced to dietary diversity than the pathway that might be expected, and have implications for how best to understand and conceptualise the tensions and synergies between addressing different aspects of malnutrition in all its forms – and suggest the importance of addressing food insecurity constraints that potentially limit the growing of nutrient-rich legume crops as well as wider increases to dietary diversity. The results also point to the importance of the income pathway and food markets in facilitating greater dietary diversity. Further consideration of these issues by policymakers and the wider agri-nutrition community will be important to advance the discussion and research of how best to design AISP and other public policy to address malnutrition in all its forms.