The objective of this study was to understand the impacts of COVID-19 crisis in agriculture and food systems in Nepal and assess the effectiveness of measures to deal with this crisis. The study draws policy implications, especially for farming systems resilience and the achievement of SDGs 1 and 2. The findings are based on (i) three panel discussions over six months with policy makers and experts working at grassroots to understand and manage the crisis, (ii) key informants' interviews, and (iii) an extensive literature review. Results revealed that the lockdown and transport restrictions have had severe consequences, raising questions on the achievement of SDGs 1 and 2, especially in the already vulnerable regions dependent on food-aid. This crisis has also exposed the strengths and limitations of both subsistence and commercial farming systems in terms of resiliency, offering important lessons for policy makers. Traditional subsistence farming appears to be somewhat resilient, with a potential to contribute to key pillars of food security, especially access and stability, though with limited contributions to food availability because of low productivity. On the other hand, commercial farming - limited to the periphery of market centres, cities, and emerging towns and in the accessible areas - was more impacted due to the lack of resilient supply networks to reach even the local market. Lower resiliency of commercial farming was also evident because of its growing dependence on inputs (mainly seeds and fertilizer) on distant markets located in foreign countries. The observation of crisis over eight months unleashed by the pandemic clearly revealed that wage labourers, indigenous people, and women from marginalized groups and regions already vulnerable in food security and malnutrition suffered more due to COVID-19 as they lost both external support and the coping mechanisms. The findings have implications for policies to improve both subsistence and commercial farming systems – in particular the former by improving the productivity through quality inputs and by diversifying, promoting and protecting the indigenous food system, while the latter through sustainable intensification by building reliant supply network linking farming with markets and guarantying the supply of inputs.