The growing landscape of cell and gene therapies necessitates a shift toward automated cell processing to circumvent limitations observed in traditional manual methods. This study explores the challenges encountered during the manufacturing and in-house quality control testing of Cell and Gene Therapy Products (CTGTPs) in two separate GMP laboratories, comprising of five Grade B processing suites within the Cell and Gene Therapy Facility, Health Sciences Authority, Singapore. Drawing from our own experience with various single and modular platforms such as CliniMACS Prodigy, MACSQuant, and Automated Haematology Analyser, this study highlights various hurdles we faced due to software, hardware, equipment and material issues; manpower and facility constraints; and regulatory and GMP standards requirements. Specific challenges identified in the study include system glitches, difficulties in equipment and material qualification, limited manpower (i.e., training of manpower in this developing field and requirement of continuous monitoring by trained personnel), facility downtime and 21 CFR part 11 compliance. Some in-house strategies to manage these challenges include having improvised monitoring systems and incorporating Westgard QC to reduce random or systematic error in our haematology analyser. Future considerations may include having better quality starting cell materials for scalability, reduction of production costs, and incorporating detailed automated equipment self-checks. Addressing these challenges is vital for enhancing automated cell processing reliability and expanding its potential in advancing cell and gene therapies and the sustainability of these processes.