Introduction. Apple fruit containsmany compounds with positive effects on human health but even smallpesticide residues from integrated production cause many food safety issuesfor consumers. Materials and methods. The apple fruits fromdifferent types of production: organic, integrated and two combinedsystems were analyzed. Their contents of sugars and organic acidswere quantified with the use of HPLC with RI and UV detectors, andphenolic contents from apple skin and pulp were detected with HPLC-MS.Apple quality was also determined in terms of weight, firmness andcolor. Results. Organically produced fruits had 14%lower weight than integrated fruits, as well as 15% higher firmnessand less green skin color than apples from the other three treatments.Among primary metabolites, the sum of sugars (fructose, glucose,sucrose and sorbitol) as well as organic acids (malic and citric)was highest in the integrated production treatment. Among secondarymetabolites, eighteen individual phenolic compounds were determinedseparately in apple peel and pulp. They were classified into four groups:hydroxycinnamic acids, flavan-3-ols, dihydrochalcones and flavonols. Themajority of the identified compounds were dependent on the applied managementsystem. Their concentrations were mainly highest in the organictreatment due to higher stress levels. The multivariate analysisof all monitored parameters placed organic production into one groupand presented a similarity among the other three management systems.