This article examines the predominant research methodologies in higher education in Ecuador, highlighting a clear inclination towards qualitative approaches, especially in the social sciences and humanities. The growing interest in mixed methodologies reflects a trend towards a more holistic understanding of the phenomena under investigation, combining qualitative depth with quantitative precision. Comparison between institutions reveals significant inequalities in access to resources and training, which impacts on the capacity to adopt advanced methodologies. Universities with better infrastructure and research support policies show greater methodological diversity and scientific output. On the other hand, universities with fewer resources tend to rely on qualitative approaches due to limitations in training and technology. The study also highlights the influence of disciplinary context and academic level on methodological choice. To improve the quality of research in Ecuador, it is necessary to strengthen training in methodologies, improve institutional infrastructure and ensure the equitable implementation of research support policies.