Heart rate (HR) was tested as a reliable index for recovery management during interval training (IT), considering its relationship with the several factors involved in respiratory, metabolic and cardiovascular homeostasis. Thirteen runners underwent two different IT sessions: at 80% and 120% of the second ventilatory threshold (VT2). Throughout both sessions HR, oxygen uptake (VO₂), carbon dioxide production (VCO₂) and pulmonary ventilation (V_E), were measured by means of a portable gas analyzer. Carbon dioxide production excess (CO_2excess), respiratory exchange ratio (RER), oxygen pulse (OP) and oxygen debt (O_2debt) were also estimated. A significant increase in HR values (144 versus 150 beats·min^–1 between the first recovery and the last, p < 0.001) was observed at 80% of the VT2 speed. At the over-threshold intensity, HR rose from 159 to 168 beats·min^–1 from the first recovery to the last (p < 0.001). OP showed a declining trend from the first to the last recovery at 80% at the VT2 speed (18.3 versus 16.4 mL·beats^–1, p < 0.05) and between the first and the last recovery in tests performed at 120% of the VT2 speed (17.8 versus 16.3 mL·beats^–1, p < 0.05). No change occurred in CO_2excess, VO₂, RER, V_E and O_2debt. On the basis of our research, the use of fixed HR as a reliable index of the established recovery is inaccurate and unfit for training. The phenomenon of cardiac drift to set the restart timing after the repetitions, i.e. by progressively increasing HR values, should be taken into account by coaches.