While women constitute a majority of Africa’s agricultural labour force, only a minority of them make decisions about income earned from harvests. Poor command over production capital –including unenforced individual rights over cultivated land and poor access to inputs such as fertiliser –is one constraint that limits women’s agency over income from agricultural outputs. This paper studies Malawi’s Farm Input Subsidy Programme (FISP) that distributed fertiliser and seed vouchers to poor agricultural households in a context of high gender inequality, a dominantly matrilineal land inheritance system and dual matrilocal and patrilocal settlement practices after marriage. Because the FISP alters households’ agricultural input combinations, de facto gender-specific land rights in matrilocal and patrilocal communities should play a smaller role in determining who has decision-making power in households. This paper estimates the heterogeneous impacts of subsidies on gendered agency patterns in matrilocal and patrilocal communities. Women have a low degree of agency in all communities, though the disadvantage is highest in patrilocal communities. Econometric models show that men have less agency in matrilocal communities than in patrilocal communities, but the FISP narrows this gap. Male household heads in matrilocal communities experience less competition from male members of their wives’ extended families when they receive the FISP. The programme therefore increases gender inequality in matrilocal decision-making to more closely resemble the pattern in male-dominated patrilocal communities. Nevertheless, women in patrilocal regions are able to leverage the returns from increased market integration to reduce their involvement in precarious ganyu labour. Targeting women as beneficiaries of the FISP is unlikely to change agency patterns in especially matrilocal communities unless women’s individual rights over cultivated land are also asserted.