Manufacturing capacity shortfalls continue to disrupt critical industries, such as pharmaceuticals, biologics, and medical devices, where stringent regulatory and quality obligations directly impact operational throughput. While global demand for essential products has intensified, the ability of manufacturers to expand capacity has been constrained not only by material and labor shortages but also by compliance-driven frictions. Regulatory frameworks such as the U.S. Food and Drug Administration’s Quality Management System Regulation (QMSR), the European Union’s revised Good Manufacturing Practice (GMP) Annex 1, the Drug Supply Chain Security Act (DSCSA), and harmonized International Council for Harmonisation (ICH) guidelines—Q9(R1), Q12, and Q13—are designed to enhance quality, traceability, and risk management. However, when integrated into legacy operations, these requirements often lengthen validation cycles, increase documentation burdens, and create bottlenecks in product release, thereby magnifying short-term capacity constraints. Recent crises, including the intravenous saline shortage following Hurricane Maria in 2017, the 2022 infant formula disruption, and delays in device approval under the Medical Device Regulation (MDR) and In Vitro Diagnostic Regulation (IVDR), demonstrate the systemic impact of regulatory obligations on capacity resilience. These cases illustrate that compliance, if poorly aligned with operational design, can depress effective throughput by 10–20%. Conversely, evidence shows that when regulatory expectations are embedded into system architecture through risk-based approaches and lifecycle change management, organizations can recover lost capacity while reducing the recurrence of deviations. This paper develops a seven-step framework—spanning regulatory concordance mapping, compliance-integrated value-stream modeling, risk-based decision analytics, lifecycle change acceleration, digital twin simulations, quality maturity uplift, and structured regulatory engagement—to diagnose and mitigate compliance-related capacity losses. Findings suggest that such integration not only restores 10–18% of throughput but also strengthens systemic resilience, reframing compliance from a constraint to a strategic enabler of sustainable manufacturing capacity.