The current world survey states that it has become a major issue of huge wastage of fruits and vegetables in our ecology and economy. The by-products of these vegetables can be a major source of nutrients with having potential phytochemical, antioxidant, and antimicrobial potential. Hence, the significance of our study is to do the comparative analysis of phytonutrients and in-vitro medicinal activity by using the discarded onion and garlic peels as sustainable resources. The results of the current study depict onion peel extracts contain highest concentration of polyphenols (174.95 ±20.42 mg GAE/g DW), flavonoids (49.97±1.77 mg QE/g DW), tannins (31.72±0.02 mg TAE/g DW), carbohydrates (30.39±1.30 mg GE/g DW), proteins (38.07±0.86 mg BSAE/g FW), whereas, garlic peel extracts contain highest concentration of antioxidants (37.54±1.05 mg AAE/g DW). Both the onion and garlic peel extract show the maximum zone of inhibition against E. coli. The outcome of the study comes up as a very innovative and beneficial way to cope up with the current life-style disorder and to reduce the risk of diseases.