Objectives in this study were to model/predict simultaneous influences of apple O2‐consumption/CO2‐production rates (RO2/CO2) and modified atmosphere packaging (MAP) (from volumetric concentrations of O2/CO2 (yO2/CO2)on microbial growth (Aerobic mesophilic bacteria, AMB; Enterobacteriaceae, EBac) in 2 fresh‐cut apple cultivars treated with five anti‐browning treatments and stored in refrigerator. Growth of both microorganisms was best predicted by length of shelf‐life, RO2/CO2, and yO2/CO2.With AMB/EBac growth, cultivar's RO2 decreased together with yO2 in packaging. Similarly, with microbial growth RCO2 dropped, while simultaneously yCO2increase was observed in package. Regression coefficients ratios for AMB‐respiration models were similar to ratios for stoichiometric coefficients for respiration equation with malic acid as main substrate. Hence, presented models likely captured natural relations between predictors, and gave good estimate of AMB growth and its association with respiration in MAP. Apple browning had weak or no association with bacterial growth. Obtained models may be utilized to optimize industrial parameters with least AMB/EBac growth, hence facilitate extension of fresh‐cut apple shelf‐life. Practical Applications Relationships between fresh‐cut apples O2‐consumption/CO2‐production rates, volumetric concentrations of O2/CO2 in modified atmosphere packaging (MAP) and microbial growth (Aerobic mesophilic bacteria, AMB; Enterobacteriaceae EBac) were established and yielded mathematical models which may be utilized to optimize industrial parameters with least AMB/EBac growth, hence facilitate extension of fresh‐cut apple shelf‐life. All equations and models are publicly accessible at apple.pbf.hr or 31.147.204.87, and can be used to calculate almost every parameter relevant for apple respiration and apple browning (only for permeable systems). Additionally, users can choose their own production settings (size of package, initial volumetric concentration of gases, apple mass), and calculate optimal values (with least browning) for their fresh‐cut processes (taking into account their own packaging film and others). Therefore, results presented in this paper will likely be useful to the fresh‐cut industry.