Alterations in HPA-axis and autonomic nervous system activity have been associated with posttraumatic stress disorder (PTSD) development and maintenance and are potentially associated with trauma-focused cognitive behavioral therapy (TF-CBT) outcomes. We examined the role of salivary cortisol (sCort) and alpha-amylase (sAA) in PTSD and TF-CBT outcomes in German Armed Forces service members (N = 100). Participants categorized as PTSD patients (n = 39), previously deployed healthy controls (n = 33), and nondeployed healthy controls (n = 28) provided diurnal profiles of sCort and sAA; PTSD patients provided samples before, immediately after, and 3 months after an internet-based TF-CBT intervention. No group differences emerged regarding total daily sCort and sAA output or daily slopes, ps = .224–.897, fs = 0.05–0.24. Participants with PTSD demonstrated a significantly attenuated sCort awakening response compared to deployed, p = .021, d = 0.59, but not nondeployed controls, p = .918, d = 0.08. Moreover, a significantly steeper sAA awakening response emerged in PTSD patients, p = .034, d = 0.67, and deployed controls, p = .014, d = 0.80, compared to nondeployed controls. From pretreatment to posttreatment (n = 21) and posttreatment to follow-up (n = 14), stable sCort, ps = .282–.628, fs = 0.34–0.49, and sAA concentrations, ps = .068–.758, fs = 0.24–1.13 paralleled a nonsignificant treatment effect. Both PTSD and trauma exposure were associated with alterations in awakening responses, but further investigation is needed to determine whether the observed correspondence remains when PTSD symptoms significantly decline.