The isolation and bottom-up assembly of nano-cellulose by using microorganisms offers unique advantages that fine-tune and meet the main key design criteria of sustainability, rapid renewability, low toxicity and scalability for several industrial applications. As a biomaterial, several properties are required to maintain the quality and functional period of any product. Thus, researchers nowadays are extensively using microorganisms to enhance the yield and properties of plant nanocellulose. A microbial process requires approximately 20%–50% less energy compared to the chemical isolation process that consumes high energy due to the need for intense mechanical processing and harsh chemical treatments. A microbial process can also reduce production costs by around 30%–50% due to the use of renewable feedstocks, fewer chemical additives, and simplified purification steps. A chemical isolation process is typically more expensive due to the extensive use of chemicals, complex processing steps, and higher energy requirements. A microbial process also offers higher yields of nanocellulose with well-defined and uniform dimensions, leading to improved mechanical properties and enhanced performance in various applications, compared with the chemical isolation process, which may result in a wider range of nanocellulose sizes, potentially leading to variations in properties and performance. The present review discusses the role of different microorganisms (bacteria, yeasts and fungi) in the isolation and production of nanocellulose. The types and properties of nanocellulose from different sources are also discussed to show the main differences among them, showing the use of microorganisms and their products to enhance the yield and properties of nanocellulose isolation. Finally, the challenges and propositions regarding the isolation, production and enhancement the quality of nanocellulose are addressed.