In this study, apples inoculated with pure cultures of Rhizopus stolonifer, Penicillium expansum and Lactobacillus plantartrm were utilised as the raw material to produce apple juice concentrate. The effects of microorganisms and various processing treatments on the fumaric acid, lactic acid and patulin contents of apple juice were investigated. R. stolonifer was found to be the most responsible causative agent of fumaric acid and lactic acid. L. plantarum also produced certain amounts of lactic acid, but not as much as R. stolonifer. L. plantarum caused a significant decrease in L-malic acid content indicating the occurrence of malolactic fermentation. During this complicated biochemical pathway, a small amount of fumaric acid was also formed by L. plantarum. P. expansum produced only patulin, but did not affect the fumaric acid and lactic acid contents. Fumaric acid contents of the samples decreased throughout the processing steps excepting evaporation. The fumaric acid contents of the samples increased just after evaporation depending on the heat applied. The patulin and lactic acid contents of the samples also showed a decreasing trend throughout processing. However, L. plantarum caused a significant increase in lactic acid content just after depectinization depending on whether the appropriate time-temperature conditions for incubation were available during depectinization.