Since their independence, many countries in sub-Saharan Africa have used input subsidies to increase agricultural productivity and improve food security. We analyse the effects of both a fertiliser and a seed subsidy on farming households' land allocation among crops and crop diversity in Burkina Faso. Although previous studies investigated either the impact of a fertiliser or a seed subsidy on targeted crops, few examined the effects of both subsidies combined. Applying a correlated random-effects model with a control function approach to nationally representative, 2-year panel data collected from farming households, we find that those with access to the fertiliser subsidy allocate more land to the crops it targets (rice, maize and cotton) than non-targeted crops. Focusing on a minor crop with key agronomic and nutritional attributes, we conclude that land allocation to cowpea as the primary crop and intercrop declined with the fertiliser subsidy.The fertiliser subsidy also negatively affects crop diversity. However, we find that the cowpea seed subsidy offsets the bias of fertiliser subsidy toward fertiliser-targeted crops and enhances diversity.In developing agricultural economies, the increasing use of modern inputs, such as chemical fertiliser, has been associated with higher agricultural productivity, especially when combined with improved seed varieties and/or adequate provision of moisture through irrigation infrastructure (Erisman et al., 2008;Morris, 2007;Smil, 2002). Historically, as a reflection of infrastructural impediments, such as sparse road networks and distance from ports, farmers in sub-Saharan Africa have used fertiliser at substantially lower rates than farmers in Asia and Latin America (Heisey & Norton, 2007). Although average fertiliser usage in sub-Saharan Africa grew by 8% annually in the early 2000s (Ariga et al., 2019) and almost doubled from 2008 (12 kg/ha) to 2018 (20 kg/ha), use rates are still well below the international average of 136 kg/ha (AFAP, 2020;World Bank, 2019).Increasing the use of modern inputs has been a policy aim in many countries of sub-Saharan Africa since their independence. Low fertiliser use has been considered a key contributing factor to lagging agricultural productivity growth in sub-Saharan Africa (Morris, 2007). High fertiliser prices, often reflecting substantial transport costs in landlocked countries such as Burkina Faso, and limited access to credit are key reasons for low fertiliser use (Gro Intelligence, 2016;Morris, 2007). The first generation of government-managed subsidy programmes resulted in unsustainable fiscal burdens, and these were dismantled during the 1990s as part of the World Bank's structural adjustment programmes. However, since the Abuja Declaration on Fertiliser in 2006, 'smart' input subsidies have proliferated in sub-Saharan