In Eastern and Southern Africa (ESA), smallholder rain-fed systems are vital, yet they are challenged by land degradation, soil fertility decline, and climate risks. To address these challenges, crop diversification has been promoted as a potential pathway to enhance productivity, improve nutritional security, and offer a viable pathway out of poverty and hunger. This study explores crop diversification among 150 smallholder households in the Kasungu, Mchinji, and Lilongwe districts of Malawi, where the project Sustainable Intensification of Maize Legume Systems in East and Southern Africa (SIMLESA) has engaged the smallholder farmers in conservation agriculture (CA)-based sustainable intensification participatory research and development for seven years since 2010. This study used Simpson’s diversity index (SDI) to estimate crop diversification, and a multiple linear regression model (MLRM) to analyze how smallholder farmers’ socio-economic characteristics influence adoption. The findings show a prevalence of small farms of less than 1.5 hectares, with most farmers perceiving crop diversification as beneficial for soil fertility. Key adoption constraints include labor shortages and a lack of legume seeds. SIMLESA participants lead in crop rotations, with a 63% higher adoption rate, and show the highest crop diversity, with a 99% increase in farmers growing three crops and a 74% increase in those growing four crops compared to non-SIMLESA farmers. The SDI values were 0.39 for non-SIMLESA, 0.48 for SIMLESA neighbors, and 0.57 for SIMLESA participants. Access to NGO inputs, larger farm sizes, and participation in research programs were positively associated with diversification, while food insufficiency was negatively associated with its adoption. The study highlights the importance of integrating participatory research methods to promote development initiatives effectively.