Breath monitoring is a non-invasive, safe, and easy approach to determining the respiratory, gastrointestinal, and general health status of humans and other mammals, since metabolic end products and volatile organic compounds are present in the breath and breath condensate. Breath monitoring is carried out by sensing exhaled breath in gas phase directly or passing the exhaled breath through a chilled condenser to obtaining the exhaled breath condensate (EBC) sample in aqueous phase for further sensing. However, for both phases, the sampling conditions, such as temperature, flow rate and relative humidity, are of great consequence because of they affect the different intrinsic properties of each biomarker, such as its solubility, volatility, and stability. The development of a breath monitoring system and future algorithms for quantifying biomarker concentrations must take into account the effects of the various breath collection conditions. In this study, enzyme-based biosensors were used to measure amperometrically different levels of ethanol, hydrogen peroxide, and ammonia in exhaled breath and EBC to develop predictive models for the effects of sampling temperature on these biomarkers. Although the biomarker concentrations were found to increase with increasing temperature, the overall effect was not to be statistically significant in limited experiment data. Henry's law constants, pH and condensing temperature could significantly affect the volatility and solubility of different biomarkers. These effects will be furthered studied so that comprehensive and robust prediction models could be developed in the future and the standardization of breath sampling and sensing could be achieved.