The main objective of this study was to determine the differences in energy expenditure (EE) according to sex during and after two different squat training protocols in a group of healthy young adults. Twenty-nine Sports Sciences students volunteered to participate in this study. They attended the laboratory on four different days and completed four sessions: two sessions with 3 sets of 12 repetitions at 75% of their one-repetition maximum (RM) and two sessions with 3 sets of 30 repetitions at 50% of their 1RM. Energy expenditure was evaluated using an indirect calorimeter. Males consistently demonstrated higher EE in all sessions and intensities. The linear regression model identified a significant association between sex, BMI, and total EE across all sessions and intensities. In conclusion, males exhibited higher EE in both protocols (50% and 75% of 1RM) throughout all sessions. Furthermore, sex and BMI were found to influence EE in healthy young adults. Therefore, coaches should consider sex when assessing EE, as the metabolic response differs between males and females.