In Ecuador’s financial system, private banks and savings and credit cooperatives coexist, both playing a key role in financial intermediation and the economic inclusion of traditionally underserved sectors. During the COVID-19 pandemic, these institutions faced unprecedented challenges that tested their adaptability and operational efficiency. In this context, the present study evaluates the technical efficiency of banks and cooperatives in Ecuador over the 2015–2023 period, using a combined approach involving Data Envelopment Analysis (DEA) and mixed linear models (MLMs). A longitudinal and comparative methodology is adopted, allowing for the analysis of efficiency trends over time and the identification of their main structural determinants. The results show that cooperatives exhibit a higher average technical efficiency than banks, as well as greater resilience during the health crisis. The analysis reveals that operating expenses negatively impact efficiency, while equity and social capital show no significant effects. By combining DEA and MLMs, the study offers a more comprehensive and nuanced understanding of the factors influencing efficiency, underscoring the importance of tailored policies and institutional strategies focused on resource optimization and continuous improvement. The study concludes that efficiency does not rely solely on size or asset volume, but rather on managerial capacity and organizational adaptability in complex and changing environments.