The study purpose was to determine the relationship of resting heart rate variability (HRV) and testosterone to cortisol (T:C) ratio, along with the diagnostic ability of HRV to assess changes in T:C ratio during a 9-week high-intensity functional training intervention. Eight recreationally-active men (n = 4, age 24.25 +/- 1.75 yrs, height 181.25 +/- 3.86 cm, weight 79.68 +/- 11.66 kg) and women (n = 4, age 26 +/- 3.6 yrs, height 164.25 +/- 3.3, weight 73.4 +/- 8.42) completed daily HRV measurements (HRVdaily) using photoplethysmography via a commercially-available smartphone application along with weekly saliva samples. Saliva samples were analyzed for concentrations of testosterone (T) and cortisol (C) via enzyme-linked immunosorbent assays. Upon study completion 72 data points were available, due to participant compliance and inadequate saliva sample, 67 matched pairs of HRV and T:C ratio were analyzed. A statistically significant negative relationship (n = 67, r = -.315, p < 0.05) was found between HRVdaily and saliva T:C ratio concentrations within aggregate data. Individual participant relationships showed considerable variability (r = -0.101 - 0.665, p = 0.103 to 0.829 The model which best explained the data resulted in AIC = 130.247 with factors HRVdaily (beta = -0.218, 95%CI = -0.391, -0.044, t = -2.46, p < 0.05), Sex (beta = 0.450, 95%CI = -0.214, 1.114, t = 1.113, p = 0.242), and Group (beta = -0.394, 95%CI = -1.089, 0.302, t = -1.11, p = 0.311). Diagnostically, HRVdaily demonstrates excellent sensitivity (95%), but poor specificity (5%) for detecting meaningful changes in T:C ratio. Assessment of HRVdaily may be a clinically valid proxy measure for monitoring hormonal changes throughout a training intervention.