Cellular heterogeneity plays a crucial role in biotechnological processes, significantly influencing metabolic activity, product yield, and process consistency. This review explores the different dimensions of cellular heterogeneity, focusing on its manifestation at both single-cell and population levels. The study examines how factors such as asymmetric cell division, age, and environmental conditions contribute to functional diversity within cell populations, with an emphasis on microorganisms like yeast. Age-related cellular heterogeneity, in particular, is highlighted for its impact on metabolic pathways, mitochondrial function, and secondary metabolite production, which directly affect bioprocess outcomes. Furthermore, the review discusses advanced techniques for detecting and managing heterogeneity, including surface marker-based approaches, which utilize proteins, polysaccharides, and lipids, and label-free methods that leverage cellular volume and physical properties for separation. Understanding and controlling cellular heterogeneity is essential for optimizing industrial bioprocesses, improving yield, and ensuring product quality. The review also underscores the potential of emerging biotechnological tools, such as real-time single-cell analysis and microfluidic devices, in enhancing separation techniques and managing cellular diversity for better process efficiency and robustness.