Brown rot (BR) in relation to codling moth damage (CMD) is a key issue in apple production but the impact of these pests has not been assessed jointly. In addition, categorising cultivar reaction to these two pests for sustainable production systems could be essential for improving pest management. Therefore, in a 12-year study, 27 apple cultivars (9 scab-resistant, 9 commercial, and 9 old) were assessed for their reactions to BR in relation to CMD in integrated and organic production systems, and classified into 3 categories (“low”, “medium”, and “high”) based on their season-long BR and CMD incidences. Then the 12-year temporal BR and CMD progresses in each category were analysed by fitting three-parameter logistic functions to process data and then by deriving 5 model variables for BR and CMD incidences. Here, we showed BR-CMD relationships in both production systems, which indicated that final BR and CMD incidences were significantly higher in organic systems. Our results show that season-long BR and CMD incidences were “low” for most resistant cultivars, and “medium” or “high” for most commercial and old ones. The area under the disease and pest progress curves indicated consistent differences among all categories in both production systems; and they were used to differentiate cultivar reactions to BR and CMD. Based on these categories and BR-CMD relationships, here we developed a new brown rot and codling moth forecasting and management strategy (BRCM-FMS). BRCM-FMS and general pest management programme (GPMP) were then compared in an additional 4-year study. This was the first study to show that the BRCM-FMS reduced annual spray applications by 21.4–41.7% in integrated and 12.5–31.3% in organic production system compared to GPMP. Disease incidences in the two programmes were similar in all years, production systems and classification categories. Less sprays and similar disease incidences provide economic and environmental benefits for growers.