Heart rate variability (HRV) may be useful for prescribing high-intensity functional training (HIFT) exercise programs. This study aimed to compare effects of HRV-guided and predetermined HIFT on cardiovascular function, body composition, and performance. Methods: Recreationally-active adults (n = 55) were randomly assigned to predetermined HIFT (n = 29, age = 24.1 ± 4.1 years) or HRV-guided HIFT (n = 26, age = 23.7 ± 4.5) groups. Both groups completed 11 weeks of daily HRV recordings, 6 weeks of HIFT (5 d·week-1), and pre- and post-test body composition and fitness assessments. Meaningful changes in resting HRV were used to modulate (i.e., reduce) HRV-guided participants’ exercise intensity. Linear mixed models were used with Bonferroni post hoc adjustment for analysis. Results: All participants significantly improved resting heart rate, lean mass, fat mass, strength, and work capacity. However, no significant between-groups differences were observed for cardiovascular function, body composition, or fitness changes. The HRV-guided group spent significantly fewer training days at high intensity (mean difference = −13.56 ± 0.83 days; p < 0.001). Conclusion: HRV-guided HIFT produced similar improvements in cardiovascular function, body composition, and fitness as predetermined HIFT, despite fewer days at high intensity. HRV shows promise for prescribing individualized exercise intensity during HIFT.