The current study aimed to analyze the effects of physical conditioning inclusion on apnea performance after a 22-week structured apnea training program. Twenty-nine male breath-hold divers participated and were allocated into: (1) cross-training in apnea and physical activity (CT; n = 10); (2) apnea training only (AT; n = 10); and control group (CG; n = 9). Measures were static apnea (STA), dynamic with fins (DYN) and dynamic no fins (DNF) performance, body composition, hemoglobin, vital capacity (VC), maximal aerobic capacity (VO2max), resting metabolic rate, oxygen saturation, and pulse during a static apnea in dry conditions at baseline and after the intervention. Total performance, referred as POINTS (constructed from the variables STA, DNF and DYN) was used as a global performance variable on apnea indoor diving. + 30, +26 vs. + 4 average POINTS of difference after-before training for CT, AT and CG respectively were found. After a discriminant analysis, CT appears to be the most appropriate for DNF performance. The post-hoc analysis determined that the CT was the only group in which the difference of means was significant before and after training for the VC (p < 0.01) and VO (p < 0.05) variables. Inclusion of physical activity in apnea training increased VC and VO2max in breath hold divers; divers who followed a mixed training, physical training and hypoxic training, achieved increased DNF performance.