The aim of this study was to determine the effect of endurance training individually guided by objective (Heart Rate Variability-HRV) or self-report measure of stress (DALDA-questionnaire) in comparison to predefined endurance training prescription for improving endurance performance in recreational runners. After a 2-week preliminary baseline period to establish resting HRV and self-reported measure of stress, thirty-six male recreational runners were randomly assigned to HRV-guided (G(HRV;) n = 12), DALDA-guided (G(D); n = 12) or predefined training (G(T); n = 12) prescription groups. Before and after 5-weeks of endurance training, participants performed a track field peak velocity (V(peak_TF)), time limit (T(lim)) at 100% of V(peak_TF) and 5 km time-trial (5 km TT) tests. G(D) lead to higher improvements in V(peak_TF) (8.4 +/- 1.8%; ES = 1.41) and 5 km TT (-12.8 +/- 4.2%; ES = -1.97), than G(HRV) (6.6 +/- 1.5% and -8.3 +/- 2.8%; ES = -1.20; 1.24) and G(T) (4.9 +/- 1.5% and -6.0 +/- 3.3%; ES = -0.82; 0.68), respectively, with no differences for T(lim). Self-report measures of stress may be used to individualize endurance training prescription on a daily basis leading to better performance enhancement, which may be used with HRV for a holistic understanding of daily training-induce adaptations.