The extensive cultivation and processing of citrus fruits is associated with significant production of citrus by-products including peels, seeds, pulp, and pomace. This organic waste facilitates various microbial reaction and greenhouse gases emission posing serious environmental threats. Incineration and land filling has been extensively practiced in past years for citrus waste management but these traditional approaches are not eco-friendly and cost-effective. However, the integration of circular bioeconomy in waste management has emerged as sustainable strategy. Citrus waste is an excellent source of various nutritional and bioactive components, hence proper valorization not only mitigates environmental hazards but also provide economic benefits. In agriculture sector, citrus waste found implications as natural fertilizer and soil amendments due to its nutritional profile and physiochemical properties. The studies suggested citrus waste as sustainable and cost-effective substitute of synthetic fertilizer. This chapter is focused on various citrus waste categories, their chemical profile and their applications as bio-fertilizer and soil amendments in agriculture.