We examined gender-based household welfare differences in Ghana among smallholder households. We measured disparities in welfare outcomes (food poverty, vulnerability, and food consumption inequality) across male and female household heads and identified the set of covariates influencing them. The study utilizes a dataset from a farm household survey undertaken in Northern Ghana from October to December 2018. A multistage sampling approach was adopted in selecting 900 farm households. The Oaxaca-Blinder mean and Recentered Inference Function decomposition techniques highlighted the sources of gender differentials in household welfare outcomes. The findings indicate a significant gap in food consumption expenditure per capita and household dietary diversity scores between male- and female- headed households, and these gaps are as high as 28.2% and 18.1%, respectively. However, there are no statistically significant differences in vulnerability to food poverty between male- and female-headed households. The Lorenz curves confirm inequality in gendered households' food consumption expenditure and dietary diversity scores. This study highlights the existence of systemic female-headed household vulnerability to food poverty in Ghana. This study provides significant evidence of the need for policymakers to address food systems' structural deficiencies and inequalities with gender in mind. © The Author(s), under exclusive licence to Springer Nature B.V. 2022.