Maternal and child undernutrition remain major public health problems in Nepal. Suaahara is a USAID-funded multi-sectoral nutrition programme aiming to strengthen local nutrition governance to reduce maternal and child undernutrition, among other objectives. The purpose of this study is to present findings from a recent qualitative evaluation of Suaahara II's influence on the decentralised implementation of Nepal's Multi-sectoral Nutrition Plan (MSNP) and identifying gaps and areas for improvement at the federal, provincial, and local levels to strengthen nutrition governance. This study employed multiple qualitative methods, engaging over 100 multi-sectoral nutrition stakeholders across three levels of government and eight districts. Thematic qualitative analysis was employed to identify emergent and salient themes, which were triangulated with other secondary data sources. Suaahara II had a positive influence on strengthening horizontal coordination for implementing the MSNP and effectively leveraged existing networks to strengthen implementation of nutrition-focused activities at the municipal level. Although there was an observable increased demand for nutrition budgets attributable to Suaahara II activities, sufficient allocation and utilisation, particularly in non-health sectors, did not meet these levels. Nepal's shift to federalism hindered vertical coordination of MSNP implementation. Some formal coordination mechanisms were strengthened, but variation in their effectiveness to strengthen horizontal and vertical coordination to implement MSNP activities continues. Finally, limited government ownership over nutrition activities and facilitating multi-sector coordination to implement the MSNP threatened sustainability of Suaahara II's outcomes on nutrition governance. Future programmes should continue to build on the progress made under Suaahara II, and specifically aim to address challenges in vertical coordination to strengthen nutrition governance in Nepal.