Background and Objectives: Particulate Matter (PM), particles of variable but small diameter can penetrate the respiratory system via inhalation, causing respiratory and/or cardiovascular diseases. This study aims to evaluate the association of environmental particulate matter (PM2.5) and black carbon (BC) with respiratory health in users of different transport modes in four roads in Bogotá. Materials and Methods: this was a mixed-method study (including a cross sectional study and a qualitative description of the air quality perception), in 300 healthy participants, based on an exploratory sequential design. The respiratory effect was measured comparing the changes between pre- and post-spirometry. The PM2.5 and black carbon (BC) concentrations were measured using portable devices. Inhaled doses were also calculated for each participant according to the mode and route. Perception was approached through semi-structured interviews. The analysis included multivariate models and concurrent triangulation. Results: The concentration of matter and black carbon were greater in bus users (median 50.67 µg m−3; interquartile range (–IR): 306.7). We found greater inhaled dosages of air pollutants among bike users (16.41 µg m−3). We did not find changes in the spirometry parameter associated with air pollutants or transport modes. The participants reported a major sensory influence at the visual and olfactory level as perception of bad air quality. Conclusions: We observed greater inhaled doses among active transport users. Nevertheless, no pathological changes were identified in the spirometry parameters. People’s perceptions are a preponderant element in the assessment of air quality.