Food loss and wastage occur in large quantities globally every year and it occurs in the entire supply chain right from the production to the processing stage. The loss of food is due to various factors like adopting traditional cultivation practices, low investment in the food sector, and more loss from poor pests and disease management of agricultural crops. The most important and major cause is due to microbial spoilage; fungi are most harmful to the consumers and also to the agriculture sector. Synthetic chemical strategies can prevent fungal growth and may reduce wastage but still causes accumulation of chemical substances in the environment and food chain in a long run. For these reasons, the use of bio-control technologies can be a great solution to agriculture and food sector as well. In view of this, the present study has been conducted using an efficient Azotobacter species, which belongs to the PGPR group. In this study, antifungal compounds produced by Azotobacter have been extracted by following solvent extraction protocols and identified using GCMS methods. The antifungal compounds were tested against the major fungal pathogens viz., Aspergillus, Fusarium, and Penicillium species. The metabolites produced by Azotobacter species were efficient in controlling the growth of the fungal species. These compounds can be used as a potential bio-preservative in the food sector instead of synthetic chemicals. Thus, these compounds can further be analyzed and tested on the food sample, having a great scope in the future to replace the chemical preservatives.