Introduction: The growing complexity of biopharmaceutical products derived from genetically engineered cell lines necessitates robust quality control (QC) systems to ensure product consistency, safety, and efficacy. In Ireland, where the biopharmaceutical sector continues to expand, understanding how QC processes are applied and optimized is vital for maintaining regulatory compliance and public trust. This study explores the role of QC in genetically engineered cell line production and its influence on batch consistency, focusing on operational practices, challenges, innovations, and cost-effective strategies. Methods: A qualitative research approach was employed, guided by an interpretivist paradigm to capture the nuanced experiences of industry professionals. Data was collected through semi-structured interviews with seven QC professionals from various Irish biopharmaceutical firms. Purposive sampling ensured participants held relevant expertise. Thematic analysis was conducted following Braun and Clarke’s six-phase method, enabling the identification of patterns and themes that aligned with the study’s five objectives. Results: Six major themes and twenty-three subthemes were identified. Key findings revealed that QC significantly affects product consistency through SOP adherence, potency monitoring, and gene expression validation. Challenges included resource constraints, regulatory fragmentation, and training gaps. Innovative practices such as realtime monitoring, AI integration, and omics-based analysis are emerging as solutions, although barriers like cost and infrastructure remain. Cost-effective strategies such as multi-use systems, shared resources, and outsourcing were highlighted, especially for small-to-medium enterprises. Ethical and societal responsibilities were also seen as integral to modern QC. Conclusions: The study contributes meaningful insights into how QC is practiced in Ireland’s biopharmaceutical sector, confirming that robust, adaptive, and ethically aligned QC systems are essential for consistent and compliant biomanufacturing. It recommends harmonization of standards, investment in training, and broader adoption of innovative and lean QC practices. These findings support policy, operational, and academic improvements in global QC systems.