Worldwide industrialization leads to a high demand for energy and natural resources, high pollution, and greenhouse gas emissions, which are associated with climate change. The circular bioeconomy is based on biological resources that are transformed into services, processes, and products, which are further recycled, minimizing waste/by-products accumulation and environmental pollution. Modern biotechnology uses cellular and molecular processes to develop technologies, products, and services. Microorganisms play a key role in the development of modern biotechnology and participate in diverse fields such as environmental decontamination, agriculture, novel materials, and natural bioproducts. The genomics and bioinformatics of organisms have revolutionized biology, allowing the prediction of biological circuits and pathways for the degradation and synthesis of a wide range of biomolecules and their regulation. Microbial genomics opens the door to biotechnological applications, reducing significantly the research and development efforts. In this review, the sailing routes from the biodiversity through microbial genomics to biotechnological applications of bioremediation, agricultural bioproducts, bioplastics, and natural bioproducts will be analyzed. The contributions of these biotechnological fields to the circular bioeconomy are discussed. Hotspots and achievements in these fields and their potential future developments are highlighted toward a circular bioeconomy, which is essential for the sustainable development of our society.