The increasing demand for energy security and environmental sustainability has intensified efforts to transition from fossil fuels to renewable energy sources such as biofuels and bioenergy. The production of biofuels involves complex upstream and midstream processes, in which microorganisms play a pivotal role. However, conventional microbial hosts used in these processes face several challenges, including contamination risks, high energy and freshwater demands, complex sterilization protocols, and significant resource-intensive operations. These limitations hinder the cost-effectiveness and scalability of biofuel production, making it difficult to compete with fossil fuel markets. To address these challenges, next-generation industrial biotechnology (NGIB) has been emerged, which focuses on the use of extremophilic microorganisms that are capable of thriving in extreme environmental conditions. Extremophiles possess unique metabolic pathways and enzymes that enable efficient biomass conversion under harsh conditions, such as high salinity, extreme pH, or high temperatures, without the need for energy-intensive sterilization. Advances in genetic and metabolic engineering, such as CRISPR/Cas9 technologies, have further enhanced the bioenergy potential of extremophiles, optimizing their metabolic traits for higher biofuel yields and resource efficiency. This chapter explores the technological interventions in bioengineering extremophilic microorganisms, highlighting their transformative potential in revolutionizing biofuel and bioenergy production.