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The COVID-19 pandemic has substantially impacted mental health—workers at institutions are not exempt. In our research, from positive organizational psychology, specifically from the healthy and resilient organization (HERO) model, we analyzed the relationship between healthy organizational practices−engagement and workers’ burnout, and evaluated the mediation role of engagement between healthy organizational practices and worker burnout levels during the COVID-19 pandemic, through structural equation models of a cross-sectional survey-based study. We collected data from a sample of 594 Chilean workers. Our results of the correlations and structural equations demonstrate the relationship between PHOs with engagement (β = 0.51; p < 0.001) and burnout (β = −0.44; p < 0.001), in addition to the mediating effect of engagement between HOP with burnout (β = −0.66; p < 0.001). In conclusion, our findings suggest that healthy organizational practices promoted worker engagement and decreased worker burnout during the COVID-19 pandemic, contributing to the postulates of the HERO model. In addition, we were able to visualize a similar scenario, which showed that burnout during a pandemic decreases when worker engagement mediates the relationship with HOP.