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Forests provide a wide range of ecosystem services, including the provision of natural resources, regulation of atmosphere–land surface interactions, and support of social and cultural activities. Atmospheric deposition of reactive nitrogen (N deposition) represents an important nutrient input to forest ecosystems; however, most nitrogen-addition experiments fail to emulate the chronic, canopy-level inputs that occur under real-world conditions. Across the Alps, total nitrogen deposition has steadily declined since the late 1980s, but current annual deposition remains at medium to high levels (on average ~15 kg N ha⁻¹ yr⁻¹). Understanding how nitrogen deposition affects Alpine forests—particularly against a backdrop of declining inputs—is therefore critical for anticipating future forest functioning and ecosystem service provision. Meanwhile, most existing studies examine the effects of nitrogen deposition on a limited number of forest functions, implicitly assuming that, after accounting for (a)biotic drivers, residual variation in the focal functions is independent of other, unexamined forest functions. Given the complexity of forest ecosystems and the exchange of mass and energy across ecological processes, this assumption of independence of intrinsic interactions among forest functions is likely violated, potentially leading to biased inference. Here, we leverage long-term Swiss forest inventory data spanning broad environmental gradients and jointly model 13 forest functions within a multivariate framework that explicitly captures trade-offs and latent relationships among functions. We show that inference on the effects of nitrogen deposition differs substantially between univariate and multivariate models, including a sign flip of the inferred impact of nitrogen deposition on some key functions (such as bird diversity). Our results highlight the importance of viewing forests as emergent ecosystems and demonstrate that multivariate approaches provide a suitable basis for assessing global change effects. By integrating expert-based evaluations of the relative importance of individual forest functions to different ecosystem services, we further quantify the marginal impacts of historical nitrogen deposition on forest ecosystem services, offering insights directly relevant to forest management and policy.