Agriculture, a cornerstone of Nepal’s economy, is dominated by smallholder farmers cultivating staple crops under resource and input constraints, leading to declining productivity amid rapid population growth and urban migration. This study explores the role of agricultural diversification in enhancing dietary diversity and improving smallholder livelihoods using panel data from the Nepal Household Risk and Vulnerability Survey (2016–2018). Analysis through the Simpson diversification index and food consumption scores reveals a strong positive correlation between agricultural diversification and dietary diversity. Key determinants include market access, irrigation systems (rainfed or canal-based), input availability (fertilizers and labor), and land type. Dry season crop diversification was positively associated with dietary diversity, while market access showed a significant negative impact on dietary diversity as distance increased. Upland areas exhibited higher potential for diversification, especially in the dry season, driven by improved access to inputs and irrigation. Policy recommendations highlight the need to enhance infrastructure in upland regions, improve market access, and ensure input availability, particularly fertilizers and labor, to support seasonal diversification. Such measures are essential for strengthening food security, nutritional diversity, and economic resilience among smallholder farmers in Nepal.