Global trends toward physical inactivity and the replacement of healthy dietary behaviors with unhealthy food consumption, particularly in late adolescence, were commonly observed. Thus, the aim of this work was twofold: (1) to examine congruence between PAPs and DPs by identifying sex differences in healthy and unhealthy behaviors and (2) to assess the explanation behind why certain participants were classified into clusters using BMI and fat mass covariates. Late adolescents (19–21 years of age, n = 107) were selected to study. PAPs and DPs were assessed with questionnaires (IPAQ, QEB) and body height, weight, and fat mass percentage were self-reported (the accuracy and reliability of self-reported data were empirically verified). A cophylogenetic approach with several clustering procedures (heatmaps and tanglegrams) was the way to solve the stated problems. Results showed that students achieved the minimal level of physical activity, lower than students from other regions in Poland, Czech Republic, or Germany. There was congruence between PAPs and DPs in some males’ and females’ behaviors. Significant similarities in sex patterns of behaviors were revealed (Mantel tests–PAPs: r = 0.70, p < 0.001; DPs: r = 0.84, p < 0.001). Similarities in PAPs were related to transportation cycling and school/work activities behaviors. Non-healthy triads in dietary behaviors were found: fast-food, sweetened beverages, and alcoholic drinks in the first, and sweets, fried meals, and yellow cheese in the second. One healthy diad was revealed: vegetables and fruits. Only females’ dietary behaviors were reflected in body mass index (F = 3.19, p = 0.049), percentage of body fat (F = 3.87, p = 0.027), and fat mass index (F = 3.83, p = 0.028). The usefulness of the cophenetic approach in patterns study was verified. Sex similarities and specific disparities could help preparing targeted tailored intervention programs that improve healthy habits in late adolescents. This is especially important in relation to females, who more strongly reflected dietary behaviors in body composition.