Hydroponics was considered an effective method to practice sustainable agriculture. However, very few studies were carried out related to the microbial and heavy metal safety assessment of hydroponically grown produce. So the microbial and heavy metal quality of hydroponically grown produce needs to be paid attention. The present study's objective was to address microbial and heavy metal safety assessment of basil and coriander grown hydroponically compared with soil-grown. Such data could be useful while proposing a scientifically validated report for consumers and farmers to reduce foodborne illness and food poisoning risk. The microbial study was carried out in three steps, that is, primary screening, secondary screening, and MALDI-TOF biotyper based confirmation, whereas heavy metals were analyzed using ICP-OES. Results from a study of the comparative analysis showed that basil and coriander collected from the hydroponic farm as well as soil farms had no pathogenic bacteria such as Salmonella spp. Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Shigella spp., and Campylobacter. The basil was not found to contain pathogens, yeasts, and molds. However, the coriander sample collected from soil-grown contained Enterobacter cloacae, Klebsiella pneumoniae, and Pseudomonas aeruginosa. In the case of heavy metal assessment, the hydroponically grown contain no heavy metal content except copper, which is present within the permissible limit. However, soil-grown basil and coriander had heavy metal content more than the permissible level. This study can infer that hydroponically grown herbs' microbial and heavy metal safety was better than soil grown.