This study investigates the global effectiveness of anti-corruption agencies (ACAs) and supreme audit institutions (SAIs) in reducing public sector corruption, addressing a significant empirical gap in how institutional autonomy correlates with long-term corruption perceptions. Utilising a panel dataset of 1,872 observations from 2012 to 2024, the research employs Fixed Effects and Random Effects models. Anchored in Principal–Agent theory, this analysis engages with the enduring debate over whether formal institutional independence effectively translates into substantive performance outcomes, as further underscored by Meagher (2005) and Doig (2017), who emphasise the persistent gap between formal mandates and actual effectiveness in anti-corruption institutions. Our findings reveal that while the autonomy of these bodies significantly associates with improved Corruption Perceptions Index (CPI) scores, this relationship is non-linear and highly conditional. Specifically, the association diminishes when adjusted for democratic stock, suggesting that democracy acts as a catalytic mechanism that transforms formal legal autonomy into functional accountability. Furthermore, the research extends current literature by identifying a synergistic effect between ACAs and SAIs, demonstrating that their coordinated independence further correlates with enhanced integrity outcomes. Ultimately, the results underscore that institutional design alone is insufficient unless embedded within democratic ecosystems that provide the necessary transparency and civil oversight to safeguard institutional performance.