Studies of pesticide use on commercial fruits are limited in Nepal. We surveyed the experiences and opinions of banana farmers in Nepal and monitored pesticide residues in apples and bananas. We monitored the residual status and associated health risks of 51 multi-group pesticides using Liquid Chromatography Triple Quadrupole Mass Spectrometry. Apple and banana samples were collected from different districts, farms, markets, and seller categories (our farm to fork survey). We found a significant bivariate positive correlation between farmers’ knowledge of pesticide negative effects and safety-promoting behavior among farmers. Residues of tebuconazole, difenoconazole, propargite and imidacloprid were most frequently detected. Of all the detected pesticides, propargite showed the highest concentration in apples, exceeding regulatory maximum residue limits (MRLs) in 24% of the samples. Epoxiconazole, tebuconazole, imidacloprid, quinalphos, fenpropathrin and bifenthrin in apples, and metalaxyl and imidacloprid in bananas also crossed their MRLs. Dietary exposure to pesticides among children and adults was estimated based on a hazard quotient and hazard index by using lower-bound and upper-bound approaches. Our results indicated that children consuming apples with residues of propargite are exposed to the greatest pesticide hazard.