Forests are an important source of environmental services and livelihoods in Africa, thus it is important to determine potential drivers of forest loss. Over recent decades, forest cover has been declining steadily in Malawi. This paper attempts to evaluate the influence of agricultural input subsidies on forest conversion in Malawi. A two-stage regression model analysis of 2009 farm survey data from Chimaliro and Liwonde Forest reserves in Kasungu and Machinga districts, respectively, did not reveal direct evidence of policy-induced forest clearing for agricultural expansion. Instead, subsidy-induced agricultural intensification of food crops, especially maize, appeared to have reduced the rate and extent of forest clearing among households in Malawi compared with households not benefiting from subsidies. However, indirect negative impacts on forests arose due to offtake of trees to construct drying sheds for tobacco, a local cash crop. These findings have implications for designing strategies for simultaneously conserving forests while promoting food security in rural areas, and shed light on the direct and indirect effects of input subsidies.