Background: Early diagnosis of post-operative complications is an urgent task, allowing timely prescribing of appropriate therapy and reducing the cost of patient treatment. The purpose of this study was to determine whether an integrated approach based on clinical data, along with metabolites and biomarkers, had greater predictive value than the models built on fewer data in the early diagnosis of post-operative complications after cardiac surgery. Methods: The study included patients (n = 62) admitted for planned cardiac surgery (coronary artery bypass grafting with cardiopulmonary bypass) with (n = 26) or without (n = 36) post-operative complications. Clinical and laboratory data on the first day after surgery were analyzed. Additionally, patients’ blood samples were collected before and on the first day after surgery to determine biomarkers and metabolites. Results: Multivariate PLS-DA models, predicting the presence or absence of post-operative complications, were built using clinical data, concentrations of metabolites and biomarkers, and the entire data set (ROC-AUC = 0.80, 0.71, and 0.85, respectively). For comparison, we built univariate models using the EuroScore2 and SOFA scales, concentrations of lactate, the dynamic changes of 4-hydroxyphenyllactic acid, and the sum of three sepsis-associated metabolites (ROC-AUC = 0.54, 0.79, 0.62, 0.58, and 0.70, respectively). Conclusions: The proposed complex model using the entire dataset had the best characteristics, which confirms the expediency of searching for new predictive models based on a variety of factors.