This study analyzes the effects of customer management and operations/logistics management with suppliers on the profitability of micro, small, and medium enterprises (MSMEs) during the COVID-19 health crisis in Costa Rica. The researchers collected data between February and May 2021 and used a multinomial regression model to test their theoretical model. The results indicate that higher perceived problems in customer-firm relationships and operations/logistics management significantly impact the profitability of MSMEs. Notably, small and medium enterprises are more affected in terms of profitability than microenterprises when facing more significant issues in customer management. The study underscores the importance of enhancing operational capacity during crises and highlights the need for managers to acquire new competencies to face future adverse scenarios.