This study analyzes the research quality assurance processes in Chilean universities. Data from 29 universities accredited by the National Accreditation Commission were collected. The relationship between institutional accreditation and research performance was analyzed using length in years of institutional accreditation and eight research metrics used as the indicators of quantity, quality, and impact of a university’s outputs at an international level. The results showed that quality assurance in research of Chilean universities is mainly associated with quantity and not with the quality and impact of academic publications. There was also no relationship between the number of publications and their quality, even finding cases with negative correlations. In addition to the above, the relationship between international metrics to evaluate research performance (i.e., international collaboration, field-weighted citation impact, and output in the top 10% citation percentiles) showed the existence of three clusters of heterogeneous composition regarding the distribution of universities with different years of institutional accreditation. These findings call for a new focus on improving regulatory processes to evaluate research performance and adequately promote institutions’ development and the effectiveness of their mission.