We estimated dietary supplies of total and available protein and indispensable amino acids (IAAs) and predicted the risk of deficiency in Malawi using Household Consumption and Expenditure Survey data. More than half of dietary protein was derived from cereal crops, while animal products provided only 11%. The supply of IAAs followed similar patterns to that of total proteins. In general, median protein and IAA supplies were reduced by approximately 17% after accounting for digestibility, with higher losses evident among the poorest households. At population level, 20% of households were at risk of protein deficiency due to inadequate available protein supplies. Of concern was lysine supply, which was inadequate for 33% of households at the population level and for the majority of the poorest households. The adoption of quality protein maize (QPM) has the potential to reduce the risk of protein and lysine deficiency in the most vulnerable households by up to 12% and 21%, respectively.