Caffeine is widely consumed among elite athletes for its well-known ergogenic properties, and its ability to increase exercise performance. However, studies to date have predominantly focused on the anhydrous form of caffeine in male participants. The aim of the study was to investigate the effect of caffeinated coffee ingestion on lower-upper body muscular endurance, cognitive performance, and heart rate variability (HRV) in female athletes. A total of 17 participants (mean ± standard deviation (SD): age = 23 ± 2 years, body mass = 64 ± 4 kg, height = 168 ± 3 cm) in a randomized cross-over design completed three testing sessions, following the ingestion of 3 mg/kg/bm of caffeine (3COF), 6 mg/kg/bm of caffeine (6COF) provided from coffee or decaffeinated coffee (PLA) in 600 mL of hot water. The testing results included: (1) repetition number for muscular endurance performance; (2): reaction time and response accuracy for cognitive performance; (3): HRV parameters, such as standard deviation of normal-to-normal (NN) intervals (SDNN), standard deviation of successive differences (SDSD), root mean square of successive differences (RMSSD), total power (TP), the ratio of low- and high-frequency powers (LF/HF), high-frequency power (HF), normalized HF (HFnu), low-frequency power (LF), and normalized LF (LFnu). A one-way repeated measures ANOVA revealed that 3COF (p = 0.024) and 6COF (p = 0.036) improved lower body muscular endurance in the first set as well as cognitive performance (p = 0.025, p = 0.035 in the post-test, respectively) compared to PLA. However, no differences were detected between trials for upper body muscular endurance (p = 0.07). Lastly, all HRV parameters did not change between trials (p > 0.05). In conclusion, ingesting caffeinated coffee improved lower body muscular endurance and cognitive performance, while not adversely affecting cardiac autonomic function.