Headbox-style indirect calorimeters can robustly estimate heat production (HP) of cattle. Volumetric flow meters (VFM), originally designed to measure gas flow in residential homes, have proven to be a cost effective method to measure airflow. Effective operation of these meters requires frequent maintenance and recalibration. Additionally, the rate of airflow of a lactating dairy cow is outside of the meters designed range. The objectives of this study were to test mass flow meters (MFM) and VFM by measuring O₂ consumption and CO₂ production and to quantify the effects of incomplete gas recovery on estimated energy partitioning. Two headboxes were initially equipped with VFM and later replaced with MFM. To determine the effects of type of airflow meter on O₂ consumption and CO₂ production, ethanol (100%) was burned for 2 h. Efficiency was calculated as the proportion of O₂ and CO₂ recovered from the amount of alcohol burned. As airflow was estimated by both methods, a subsample of gas was collected into a bag. Air in each bag was analyzed using gas chromatography. Data were analyzed using a paired t-test. Recovery of O₂ tended (P = 0.12) to be greater for MFM than VFM (99.7 ± 1.16% vs. 86.8 ± 4.50%). Recovery of CO₂ was greater (P = 0.04) when using the MFM than VFM (99.0 ± 1.76% vs. 86.0 ± 2.97%). These results suggest that MFM may yield more precise measures needed for indirect calorimetry. Incomplete gas recovery can result in underestimates of HP, thereby affecting estimates of whole-animal energy use. For example, a typical Jersey cow (assuming the body weight = 450 kg, dry matter intake = 18.5 kg, milk yield = 25.0 kg/d, urinary N excretion = 225 g/d and tissue energy = 0.00 Mcal/d) a 5.0% decrease in gas recovery results in a reduction in HP by 1.30 Mcal/d and increase in tissue energy by 1.45 Mcal/d. This tissue energy translates into an increased net energy of 1.46 Mcal/d. Our results indicate that in striving for estimates of gas recovery of 95.0 ± 5.00%, MFM may be better suited for headbox-style indirect calorimetry to estimate HP in lactating cows.