Mycobacteria can be one of the main contaminants of biological products, and their presence can have serious consequences on patients’ health. Thus, specific testing is necessitated by regulations such as the European Pharmacopoeia. The current pharmacopeial reference i.e., microbial culture method cannot ensure an exhaustive detection of mycobacteria due to their growth characteristics. Additionally, the method is time-consuming and requires a continuous supply of culture media, which could be further challenging. Thus, to overcome these challenges, pharmaceutical industries need to consider alternative non-microbiological techniques to detect these fastidious, slow-growing contaminating agents. This review provides an overview of alternative methods, which could be applied within a quality control environment of biological products, and underlines advantages and limitations of these methods. Nucleic acid amplification techniques or direct measurement of mycobacteria stands out as the most suitable alternatives for mycobacterial testing in biological products.