Amidst the COVID-19 pandemic, a new bus route called the EDSA Bus Carousel was launched in Metro Manila, Philippines, in 2020. It started as a quick, ad hoc solution to the limited public transportation during the community quarantine and has since been operational. The bus route has an exclusive right-of-way on a dedicated lane called the EDSA Busway located at the innermost lanes of EDSA, one of Metro Manila’s busiest and most congested thoroughfares. Bus stations are built at the median island of EDSA, exposing commuters to heat and pollution given its outdoor setup. This study examined the passenger comfort at selected busway stations—Roosevelt, Monumento, Roxas Boulevard, and Main Avenue—during morning and afternoon peak hours. Two comfort indicators, air quality (PM2.5 and PM10) and thermal comfort (measured by the Physiological Equivalent Temperature or PET index), were analyzed. After simultaneously measuring the physical parameters at the bus stations and determining the comfort perception of the passengers through a questionnaire, results revealed unhealthy air quality for sensitive groups at Roosevelt Station, with only Main Avenue meeting air quality guidelines. Despite poor air quality, some passengers perceived their environment as comfortable. On the contrary, passengers were sensitive to temperature changes, feeling more uncomfortable as it gets hotter at stations. The thermal environments at all stations did not meet the obtained neutral and comfort temperatures, yet most felt “Comfortably Warm.” These findings offer crucial insights for EDSA Busway officials and urban planners in order to create a healthier and more comfortable space for commuters.