This study examined the effect of adopting crop diversification on nutrition outcomes of smallholder households in southwestern and northern Uganda. We constructed three models of correlates of household dietary diversity, minimum dietary diversity for women, and stunting of children aged 6–59 months. A three-year panel multi-topic dataset collected in 2012, 2014 and 2016 by USAID’s Feed the Future Nutrition Innovation Laboratory in southwestern and northern Uganda was utilized. Crop diversification was found to be positively and strongly associated with household dietary diversity, and with the probability of achieving the minimum dietary diversity for women, although the effect sizes were rather small. There was no clear association found between crop diversification and child stunting. Our findings point to an integrated approach that simultaneously addresses increasing crop diversification, access to improved farm production technology, access to nutritional knowledge, increasing formal education of mothers, increasing opportunities to do off-farm work, livestock diversification and food security to improve the nutritional outcomes of smallholder households.