Understanding the gender differences in agricultural productivity is crucial for formulating informed and effective policies to sustainably improve low productivity which characterises agriculture in Sub-Sahara Africa. Using a panel dataset from the ICRISAT led Tropical Legumes project III (2008–2013), we analyse the gender gap in the production of legumes in Malawi. Employing the Oaxaca–Blinder decomposition method allows decomposition of gender gap into the following: (i) the portion caused by observable differences in the factors of production (endowment effect) and (ii) the unexplained portion caused by differences in return to the same observed factors of production (structural effect). We conducted the empirical analysis separately for pigeonpea and groundnut. Our findings reveal that for groundnut cultivated plots, women are 28% less productive than men after controlling for observed factors of production; however, the gender gap estimated in the pigeonpea cultivated plots are not statistically significant. The decomposition estimates reveal that the endowment effect is more relevant than the structural effect, suggesting that access to productive inputs contributes largest to the gender gap in groundnut productivity, and if women involved had access to equal level of inputs, the gap will be reduced significantly. The variation in the findings for groundnut and pigeon plot suggests that policy orientation towards reducing gender productivity gap should be crop specific.