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Abstract The objective of this study was to determine whether the variability in exercise tolerance and physiological responses is lower when exercise is prescribed relative to physiological thresholds (THR) compared to traditional intensity anchors (TRAD). Ten individuals completed a series of maximal exercise tests and a series of moderate (MOD), heavy (HVY) and severe intensity (HIIT) exercise bouts prescribed using THR intensity anchors (critical power and gas exchange threshold) and TRAD intensity anchors (maximum oxygen uptake; V̇O2max). There were no differences in exercise tolerance or acute response variability between MODTHR and MODTRAD. All individuals completed HVYTHR but only 30% completed HVYTRAD. Compared to HVYTHR, where work rates were all below critical power, work rates in HVYTRAD exceeded critical power in 70% of individuals. There was, however, no difference in acute response variability between HVYTHR and HVYTRAD. All individuals completed HIITTHR but only 20% completed HIITTRAD. The variability in peak (F = 0.274) and average (F = 0.318) blood lactate responses was lower in HIITTHR compared to HIITTRAD. The variability in W′ depletion (the finite work capacity above critical power) after the final interval bout was lower in HIITTHR compared to HIITTRAD (F = 0.305). Using physiological thresholds to prescribe exercise intensity reduced the heterogeneity in exercise tolerance and physiological responses to exercise spanning the boundary between the heavy and severe intensity domains. To increase the precision of exercise intensity prescription, it is recommended that, where possible, physiological thresholds are used in place of V̇O2max.