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In 2003, the United Nations Convention Against Corruption was signed in Merida, Mexico. This initiative promised the resources and expertise necessary for combatting corruption in the developing world. Many countries across Latin America enabled their supreme audit institutions as anti-corruption agencies with the premise of holding corrupt politicians accountable. Today, scandals of corrupt mayors and governors are frequent in the press while the number of prosecuted politicians is negligible. Why do supreme audit institutions vary in their performance? This project argues that the automatization of audit institutions, a feature sold by the international community and researchers as desirable for enforcing accountability, is undermined by the politicization of audit organizations through the appointment of partisan leaders. Mexico, as the host nation of the Merida Initiative is an ideal case study given the adoption of the supreme audit institution across its 32 states. This facilitates an analysis where national level trends are constant but offers variation in the degree of autonomy assigned to each, along with frequent turnover in the head auditor position. The empirical analysis suggests that with increased decision-making discretion, partisan auditors tend to avoid applying audits and delivering sanctions. The results also point to potential best practices that may guide reformers in safeguarding organizations responsible for enforcing horizontal accountability from political influence.