Physical exercise strongly affects human metabolism and causes biochemical changes. This study aimed to investigate the relationship between routine plasma biomarker levels and recovery efficiency in soccer players during an entire competitive match season. The players participating in the study were divided into a midfielder/defender group (seven midfielders and seven defenders) and a goalie/substitute group (six persons—goalkeepers and players with a short cumulative match-time). The fasting capillary blood samples were taken 17–24 h after each competitive match. The blood plasma was used to determine the creatinine, urea, alkaline phosphatase, creatine kinase, lactate dehydrogenase, aspartate and alanine aminotransferase, iron and magnesium levels of the athletes. The levels of (AST) (aspartate aminotransferase), (ALT) (alanine aminotransferase) and (Cr) creatinine were higher in the midfielder/defender group than in the control group, but only AST and Cr significantly varied over time (AST decreased, and Cr increased with time). The (LDH) (lactate dehydrogenase) activity and urea level were significantly lower in the midfielder/defender group than in the goalie/substitute group, and it significantly varied over time (LDH decreased, and urea increased with time). No differences in the (CK) creatine kinase and (ALP) alkaline phosphatase activities between the groups was found, although CK increased significantly with time in the midfielder/defender group (particularly midfielders in the spring round). In midfielders, the AST activity and the iron level were significantly lower in the spring than in the autumn round. On the contrary, ALT, CK, urea and magnesium levels were significantly higher in the spring than in autumn round. A long-term measurement of biochemical parameters in elite soccer players indicated that AST, CK, LDH and creatinine levels, when analyzed together, could constitute a useful set of markers for monitoring recovery periods.