This study contributes to the evidence on the impact of agricultural policies and programmes on nutritional outcomes at the household level. We specifically examined the effect of adoption of crop diversification on household and child nutrition outcomes among small-scale farm households in South-western and Northern Uganda. We constructed two models of correlates of intermediate nutritional outcomes (Household Dietary Diversity and Minimum Dietary Diversity for Women) and one model of correlates of a final nutrition outcome (child stunting). A 3-year panel multi-topic dataset collected by Feed the Future Nutrition Innovation Laboratory as part of the Community Connector Project in Southern-western and Northern Uganda was used. In all estimations, we found that crop diversification is positively and significantly associated with Household Dietary Diversity and Minimum Dietary Diversity for Women. The findings also suggest that to increase dietary diversity, the crop diversification strategy needs to be accompanied by interventions that increase farm household’s access to improved seed varieties, and increase farm households’ nutrition knowledge. In other findings crop diversification has a negative and significant effect on child stunting when child and caregiver’s characteristics are controlled for in the estimation model.