Sex hormones are suggested to influence energy intake (EI) and metabolic hormones. This study investigated the influence of menstrual cycle (MC) and hormonal contraceptive (HC) cycle phases on EI, energy availability (EA), and metabolic hormones in recreational athletes (eumenorrheic, NHC = 15 and monophasic HC-users, CHC = 9). In addition, 72-h dietary and training logs were collected in addition to blood samples, which were analyzed for 17β-estradiol (E2), progesterone (P4), leptin, total ghrelin, insulin, and tri-iodothyronine (T3). Measurements were completed at four time-points (phases): Bleeding, mid-follicular (FP)/active 1, ovulation (OVU)/active 2, mid-luteal (LP)/inactive in NHC/CHC, respectively. As expected, E2 and P4 fluctuated significantly in NHC (p < 0.05) and remained stable in CHC. In NHC, leptin increased significantly between bleeding and ovulation (p = 0.030) as well as between FP and OVU (p = 0.022). No group differences in other measured hormones were observed across the MC and HC cycle. The mean EI and EA were similar between phases, with no significant differences observed in macronutrient intake over either the MC or HC. While the MC phase might have a small, but statistically significant effect on leptin, the findings of the present study suggest that the MC or HC phase does not significantly alter ad libitum EI or EA in recreational athletes.