Indonesia is well known as producers of many spices and condiments. In culinary world, spices ingredients used for seasoning that function as flavor enhancer, including onion and shallot. Usually the loss of fresh onions in storage is about 25 to 30% during 5 until 6 months. In order to decrease the loss of onions, the processing of onion into several products is required. Production of onions into vinegar can help it to prolong shelf life. The effect of different types of onion is observed in this research. Different autoclave time is applied to onion and shallot extract. Well diffusion assay, antioxidant analysis, total phenolic content, flavonoid analysis, mineral analysis, pH analysis, and color analysis are performed to the autoclaved onion extract to determine the best autoclave time toward onion extract. Both onion and shallot extract required 40 minutes autoclave time to go further into primary research, since increasing of autoclave time increases the removal of antimicrobial function in both extracts, total phenolic content, flavonoid content, mineral content (except Na), and antioxidant activity. In the primary research, the effect of different sugar concentration (10, 15, 20, 25 and 30%) was observed toward the quality of onion vinegar. The autoclaved onion and shallot extract was inoculated by Saccharomyces cerevisiae for alcoholic fermentation and allowed for acetic acid fermentation by adding Acetobacter aceti for 28 days to produce vinegar. The results shows that increasing of sugar concentration increases the total titratable acidity, organic acid content, sensory acceptance, density, thus reduce total alcohol content, while TPC is still in BSN (Badan Standarisasi Nasional) requirements and mineral contents tends to differ.