The impacts of climate change are evident in the agriculture sector globally. These impacts are more severe and pronounced in a mountainous country like Nepal due to the high reliance on agro-economy and subsistence-based livelihoods by smallholder farmers that increase vulnerability and risks. Several ecosystem-based adaptation measures have proved to build the adaptive capacity of both agro-ecosystems and smallholder farmers by offering simple and affordable technologies however, these are yet to be prioritized by policy and programs for scaling. In this paper, we provide science-based evidence to traditionally used practices, such as jholmal (locally prepared bio-fertilizer and pesticides) and straw mulching by comparing their efficacy in terms of yield and reduction in disease pest infestation. The study was conducted in Kavre district of Nepal during 2017 and 2018 using participatory on-farm field trials for jholmal and straw mulching designed separately with Randomized Complete Block Design for selected vegetable crops like bitter gourd and tomato. The application of jholmal showed significant increase in bitter gourd yield both at the foothill and hilltop sites compared to the farmer’s business usual practice (in 2017 and 2018, bitter gourd yield increased by 30.5% and 31.1% in foothill, while 26.6% and 28.7% in hilltops respectively). Further, a significant reduction on fruit infestation was observed in jholmal treated plots. Similarly, there was increase in tomato yield when straw mulch was used compared to the non-mulched trials (in 2017 and 2018, tomato yield increased by 16.5% and 20.3% respectively). These findings suggest that traditionally used practices have scientific basis and offer simple, affordable and climate friendly practices to improve the health of agro-ecosystem while supporting smallholder farmers to adapt to adverse impacts of climate change and build socio-ecological resilience. These practices can be also customized depending on the local context for wider adoption and scaling across Nepal and elsewhere as ecosystem-based adaptation measures for smallholder farmers.