Studying turbulent heat transfer over rough surfaces is vital for enhancing heat transfer efficiency in various practical applications. This research presents an in-depth examination of the commissioning of a heated floor boundary layer wind tunnel facility, specifically focussing on addressing the uncertainties in measuring heat transfer over rough walls. Our findings show that minor variations in the slope of the inner-scaled mean temperature profile (\(\kappa _h\)) on a heated smooth wall have a marginal effect on the estimates of friction temperature and heat transfer coefficients across a range of friction Reynolds numbers (\({900 \lesssim \textrm{Re}_\tau \lesssim 3700}\)) when using the Clauser fit method. Direct heat transfer measurements using power metres validate this conclusion. Temperature measurements over a three-dimensional sinusoidal roughness indicate constant \(\kappa _h\) within uncertainty limits across the examined range \({2300 \lesssim \textrm{Re}_\tau \lesssim 10{,}400}\), contingent on prior knowledge of the roughness’s virtual origin. Nevertheless, measuring heat transfer coefficients and roughness functions entails large uncertainty due to challenges in estimating heat losses and applying the modified Clauser method. Recommendations for enhancing accuracy in heated rough wall measurements include direct measurement of wall shear stress and heat flux, selecting low emissivity heated plates and ensuring precise control of heated wall conditions. This work also emphasises the significance of conducting a comprehensive uncertainty analysis as a valuable tool for identifying and addressing any shortcomings in the measurement facility and equipment.