During prolonged continuous exercise, the relationship between external load (e.g., running speed) and internal load [e.g., heart rate (HR)] shifts. This means, for example, that at a given running speed, the HR will continuously increase, whereas if the goal of the exercise is to maintain a constant HR, the running speed will decrease over time. The time dependence of the internal/external load relationship could lead to different acute responses and chronic adaptations depending on the exercise intensity reference method. This hypothesis was tested in the present study. Forty-three previously inactive individuals were randomized into two groups: one group (SPEED-C) trained at a speed midway between the first and second lactate threshold (v ∆ 50LT), whereas the other group (HR-C) trained at a HR midway between the thresholds (HR ∆ 50LT). Both groups performed 30 min of continuous endurance exercise 3 times per week for 8 weeks. Maximal oxygen consumption (V̇O2max) and peak treadmill speed (Vpeak) were determined by an incremental treadmill test followed by a verification test before (PRE) and after (POST) the 8 weeks of training. V̇O2, HR, speed, and rate of perceived exertion (RPE; measured with the Borg CR10) were recorded during the first and last treadmill training sessions performed in the lab. After POST, an additional simulated session was performed with the intensity adjusted to the new training level. Thirty-four participants (9 women and 7 men in SPEED-C; 11 women and 7 men in HR-C) completed the study and were included in the analysis. v ∆ 50LT/HR ∆ 50LT occurred at 74 ± 5% of HRmax, 63 ± 4% of V̇O2max, and 60 ± 4% of V̇peak in SPEED-C and at 74 ± 5 % of HRmax, 63 ± 5% of V̇O2max, and 60 ± 6 % of V̇peak in HR-C. SPEED-C showed higher speed (+1.5 km/h, p < 0.001), V̇O2 (+6.3 mL/kg/min, p < 0.001), HR (+23 bpm, p < 0.001) and RPE (+1.9 points, p = 0.002) than HR-C during the first training session. These initial differences between groups were reduced after 8 weeks of training (speed: by -0.5 km/h, p = 0.006; V̇O2: by -2.6 mL/kg/min, p < 0.001; HR: by -14 bpm, p < 0.001; RPE: (-1.7 points, p = 0.002). However, statistically significant reductions were no longer observed when the intensity was adjusted to the new training level. V̇O2max (+1.0 mL/kg/min, p = 0.021) and Vpeak (+0.8 km/h, p < 0.001) improved more in SPEED-C than in HR-C. Among the secondary physiological characteristics investigated in this study, speed at the second lactate threshold (+1.1 km/h, p < 0.001) and v ∆ 50LT (+0.5 km/h, p = 0.008) improved more in SPEED-C than in HR-C, whereas HR at the second lactate threshold improved more in HR-C than in SPEED-C (-7 bpm, p = 0.008). The exercise intensity reference method (speed vs. HR) affects acute responses and chronic adaptations in previously inactive individuals. However, training conditioning may mitigate these differences if the intensity is not constantly adjusted to the new training level.