The aim of this study was to evaluate and compare the effect of antibiotic and pesticide residues on the physicochemical properties of unifloral and multifloral honey. The mineral elements content of honey was analyzed and correlated with antibiotic and pesticide residues, and a positive correlation was found between manganese and neonicotinoids. Potassium was found to be the most abundant mineral compound. Correlations were found between mineral content, color, and the content of antibiotic and pesticide residues of honey. In meadow honey, residues of antibiotics and pesticides were undetectable. In some of the other types of honey, the maximum residue limits regulated by European legislation were exceeded. Endosulfan residue was found in mint and rapeseed, honey with 0.42 and 5.14 ng/g, respectively. Neonicotinoids were found in 27% of the analyzed honey samples. Chloramphenicol was identified only in rapeseed honey, with concentrations ranging from 0.2 ng/g to 0.8 ng/g. Nitrofurans were found in 14%, and nitroimidazoles were found in 6% of the analyzed samples. According to EU legislation that is in force, the use of antibiotics in beekeeping is not allowed. The MRLs for neonicotinoids are 50 ng/g, and for coumaphos, the maximum limit is 100 ng/g. For the other pesticide residues, the maximum limit is 10 ng/g. The results of statistical analysis obtained using principal component analysis (PCA) showed a major difference in the levels of contamination of raspberry and meadow honey and the other types of honey.