University autonomy in Bolivia, constitutionally defined as functional self-governance rather than complete institutional independence, has become a site of political manipulation by certain university leaders and political groups. This paper argues that these actors illegitimately distort the concept of autonomy to resist legitimate state oversight, transforming it from a mechanism for advancing science and knowledge into a tool for power struggles and personal benefit. Drawing on Critical Discourse Analysis, political manipulation is dissected into three core elements: illegitimate influence (discursive distortion), power abuse (control of discourse and context), and benefit-harm relationship. The analysis demonstrates how university authorities propagate a misrepresented notion of absolute independence to evade accountability. Empirical cases, including the 2021 UPEA tragedy, prolonged student leaders, and resistance to state coordination under the PDES and university regulations, reveal how this manipulation enables corruption, regulatory capture, and the stagnation of Bolivia's public university system. While political groups gain unchecked power and influence, the university community suffers diminished academic quality, innovation, and public legitimacy. The paper concludes that genuine university autonomy requires mutual University-State oversight to prevent abuse, as affirmed by the Bolivian University Executive Committee and constitutional provisions. This national issue underscores broader tensions in balancing institutional independence with public accountability in higher education.