Infection containment in the post-pandemic scenario became a top priority for healthcare engineering control staffers, especially in pneumology sectors, where the treatment of airborne infectious diseases is frequent. In Brazil, where COVID-19 left a long record of casualties, there is a lack of information on the influence of filtration systems on the maintenance of regulated operational conditions for indoor comfort in hospital environments. This paper has the following objectives: to study arrangements of filtering systems in hospital acclimatization ducts; to verify how filtering characteristics could compromise safety regulations for airflow in hospital environments; and to identify airflow stagnation points that might favor suspended viral concentrations and increase contamination risks. We used the computational fluid dynamics STAR-CCM+© software to perform numerical simulations of different cases of indoor airflow in a model corresponding to a sector of the Lauro Wanderley University Hospital (João Pessoa city, Brazil). We concluded that standards for maximum velocity are reachable despite thinner or thicker filters affecting the spread of the air. In this way, acclimatization systems are limited by a tradeoff between regulation and protection. Our findings are relevant to future technological development, interventions, safety strategies amidst contamination scenarios, and new filtration arrangements in hospital environments.