This paper explores agricultural productivity differences in Malawi arising due to differences in the gender of the plot manager based on a gender disaggregated sample of 784 maize, 232 groundnut, 212 tobacco and 199 cotton plot managers. Decomposition techniques were used to identify the relative quantitative importance of factors explaining the gender gap at the mean of the agricultural productivity distribution. This was carried out using data from the fourth Malawi Integrated Household Survey (IHS 4), which was nationally representative and collected within a multi-topic framework with emphasis on gender disaggregation of crop farming preferences. The survey was conducted by the Malawi National Statistical Office from April 2016 to April 2017 and information was collected from a sample of 12,447 households. Empirical investigation based on the Oaxaca-Blinder regression-based mean decomposition showed that gender gaps exist where men are more productive in the cultivation of both male and female dominated crops. Large and significant gender disparities were seen not only in the use of inputs (particularly fertilizer and labour) but also in the returns to those inputs. Higher levels of household adult male labour on male-managed plots, in particular, widen the gender gap. The female structural disadvantage component of the gender gap is exacerbated by gender differences in the availability of time devoted to productive activities. This is because female managers, who are just as likely to be household heads or spouses, are more likely to combine farm management with household duties including child care in the Malawian social setting.