In food and beverage sector, biotechnological applications of pectinase have been increasing day by day. However, subdued production volume and low purity of the pectinase in commercial scale still remain a challenge. As a result, researchers are continuously exploring the opportunity to express modern tools such as genetic engineering, metagenomic study, and metabolic engineering to exploit microbes as a promising source for pectinases. Although this enzyme can be found naturally in plants, microbial pectinases retained a high value preference due to its easy fermentation in different bioreactors and inimitable physicochemical attributes. Microbial pectinase has immense potential to contribute in different areas such as textile industries, pharma sector, paper, and pulp industry, environmental engineering, agricultural economics in addition to that food, and beverage industries. The assertion of gene manipulation for better production of pectinase by means of elementary molecular devices and conventional fermentation procedures has been correlated in this study to get a bird's eye view in the structure-functional relationship of the microbial pectinases.