Fruit tree production faces the major challenge of ensuring maximal productivity with due consideration for the environment and human health. The increasingly recognized concept of ecosystem service could help to address this duality. In this paper, we propose an analytical framework based on a soil crop model to investigate how agricultural management and pedoclimatic conditions affect the joint production of marketed and non-marketed ecosystem services through underlying ecosystem functions in apple orchards. The ecosystem services considered on an annual scale were soil nitrogen availability, climate regulation, water regulation and fruit production. Ecosystem functions and services were described by specific indicators that were quantified using the STICS soil crop model. This model was parameterized using data collected on two experimental apple orchard sites under conventional and low-input or organic management in southeastern France. The interdependencies between environmental components, cultural operations and ecosystem functions were dynamically integrated by the model and highlighted significant interactions between the indicators of ecosystem services. Thus, the service indicators soil organic nitrogen variation and the prevention of nitrogen denitrification and of leaching were positively correlated and in conflict with soil mean nitrate concentration and mean soil humidity. They were also linked negatively to nitrogen mineralization enhanced by irrigation and positively to soil carbon sequestration impacted by fertilization; these two functions were impacted by soil conditions. Yield and carbon sequestration presented a strong synergy and were positively correlated to nitrogen absorption increased by mineral fertilization. Globally, nitrogen fertilization management and planting density were particularly important for the delivery of multiple ecosystem services, but soil and climate effects were far from negligible, especially for nitrogen and water-related services. The ecosystem service profiles of the studied cropping systems were diversified, with contrasted profiles showing high yield and carbon sequestration but low prevention of nitrogen denitrification and of nitrogen leaching, and more balanced profiles. The STICS crop model made it possible to quantify and analyze profiles of ecosystem services and should be helpful in instrumenting the dialogue between fruit growers and other stakeholders by simulating scenarios to optimize multiple services. However, it has to be improved to address the impact of grass cover on soil functions and the long-term functioning of apple orchards.