We explore whether real-time breath analysis by high resolution mass spectrometry is suitable to monitor changes at the metabolic level due to inhaling bronchodilator medication. We compared the breath levels of metabolites in a group of patients (n = 50) at baseline and 10 and 30 min after inhalation of 200 μg salbutamol. The same procedure was performed with a group of controls (n = 48) inhaling a placebo spray. A total of 131 mass spectral features were significantly altered as a result of inhaling medication, but not after inhaling placebo. We found that homologous series of chemical classes correlated strongly with each other, strengthening the notion that certain biochemical processes can be monitored. For example, a series of fatty acids was found to be increased after salbutamol intake, suggesting lipolysis stimulation. Peaks corresponding to salbutamol, its main metabolite salbutamol-4-O-sulfate and formoterol were found to be generally increased in patients inhaling the drugs on an as-needed basis, as compared to non-medicated volunteers. Overall, these results suggest such real-time breath analysis is a useful tool for non-invasive therapeutic drug monitoring.