Waste management is one of the biggest challenges in the modern world. Untreated wastes are the potential source for greenhouse gas emission, water and soil pollution. Millions of tonnes of fruits and vegetable waste (FVW) and agricultural waste (AW) are generated every year. FVW and AW are organic in nature and are rich source of polysaccharide components. Transformation of FVW and AW to value added products becomes the current need. Polysaccharides present in FVW and AW serve as nutrients for microbes and thus industrially important enzymes such as amylase and pectinase can be produced through microbial bio-processing of organic waste. Amylases are involved in various applications like starch coating, deinking, biopolishing, desizing, modification of synthetic fibers, stain cleaning etc. Pectinases are involved in various applications like fruit juice clarification, coffee and tea fermentation, waste water treatment, bio-scouring of plant fibres etc. Legitimate administration and management of waste can also ensure a cleaner environment and in future, a zero-waste economy. This review gives insights into how FVW and AW can be successfully harnessed as raw material for the microbial production of industrially important enzymes such as pectinase and amylase. This review also provides information on types of pectinases and amylases; their application and their novel improvement strategies.