The beneficial health effects of cheese as a source of bioactive compounds with antioxidant, antimicrobial, anti-inflammatory, immunomodulatory, and analgesic effects are well known. The aim of this study is to determine the presence of pesticide residues and heavy metals in 79 cheese samples from small farms in Croatia. The samples were analyzed over a period of three years for the quality parameters of fat, protein, dry matter, salt, and pH to determine whether metrological conditions affect the quality of cheese and to test the correlation between the variables in different types of cheese. A total of 509 pesticide residues were analyzed using liquid and gas chromatography with tandem mass spectrometry. Piperonyl butoxide was found in two samples. Inductively coupled plasma with mass spectrometry was used for a metal content analysis, and Cd, Cr, Mn, Ni, and Pb were found in the range of <0.005–0.012 mg kg−1, <0.02–0.84 mg kg−1, 0.031–1.128 mg kg−1, <0.03–0.67 mg kg−1, and <0.01–0.12 mg kg−1, respectively. Cd was detected in just three samples. Mn was found in all analyzed samples. All tested samples complied with EU regulations and directives, and at the point of analysis, none posed a direct health risk for consumers. Sustainability on small farms could be ensured with the responsible use of pesticides and through a consistent and reliable supply of fresh, high-quality milk.