The past COVID-19 pandemic has created new demand and expectations for next-generation buildings. Besides proper indoor air quality (IAQ) and daylight in the indoor environment, the building should provide appropriate working conditions. Due to this pandemic, millions have spent longer hours indoors over the past few years. It is imperative to address a multi-objective and multi-function design to control air circulation in the building's shared and isolated spaces while maintaining energy efficiency, humidity control, and other performance standards. This paper analyzed two architectural design concepts that can eliminate energy usage and daylighting inefficiencies and increase the ventilation rate to reduce indoor transmission of airborne particulates and pathogens and unwanted indoor humidity. We have analyzed the impact of courtyards and atria in typical commercial buildings based on architectural principles and practical experience to create a safe and healthy indoor environment for working and living that will improve indoor protection against the past COVID-19 and future similar virus pandemics. The results show that the use of a courtyard or atrium in design builds a positive effect on controlling the indoor environment.