Citrus fruit bears a diverse and complex microbial community. Wastage of citrus fruits means the wastage of all these beneficial microbial communities. This community consists of Bacteria, fungi, and yeasts naturally existing on the surface and within the fruit. This microbiota plays a crucial role in fruit ripening, decay prevention, and flavor development. Several types of beneficial microbiota which may be isolated from citrus waste include the bacteria especially lactic acid producing bacteria (LAB), Bifidobacterium; well-known for their probiotic properties. Obtained probiotics can improve gut health, boost immune function, and potentially offer other health benefits as well as in animal feed industries. Other microbial agents from citrus waste include yeasts, like Saccharomyces cerevisiae, can be used in fermentation processes to produce valuable products like biofuels or functional foods and other Plant Growth-Promoting Bacteria (PGPB) isolated from citrus rinds can promote plant growth and improve stress tolerance in crops by employing as bio-fertilizers. This chapter focuses on the available groups of different communities of microorganisms in citrus fruits and citrus waste and effective valorization techniques for isolating and characterizing the desired microorganisms. Furthermore, despite these challenges, exciting opportunities exist, various other aspects have been discussed including (i) Development of novel probiotic formulations with targeted health benefits, (ii) Utilization of citrus waste for sustainable production of functional foods and (iii) Development of bio-fertilizers containing PGPB isolated from citrus waste to enhance agricultural productivity and reduce reliance on chemical inputs.