Multiple ecosystem functions and services are governed by the complex interplay between biotic and abiotic factors, and each function exhibits distinct sensitivities to these drivers. Consequently, simultaneously assessing various ecosystem functions alongside their environmental determinants is critical. In this study, we employed structural modeling to investigate the direct and indirect effects of biotic (tree canopy cover) and abiotic (topographic features including elevation and aspect) factors on key ecosystem functions (carbon sequestration, aboveground biomass) and soil quality. The research was conducted in semi-arid mountainous forests of the Zagros range in western Iran (Shalam), where 60 composite soil samples were systematically collected across stands differing in canopy density (open vs. closed), aspect (north vs. south), and three elevation bands (1750–1850 m, 1850–1950 m, and 1950–2050 m). Soil quality indices were derived from measured soil properties. A three-way ANOVA within a general linear model (GLM) framework, followed by Duncan’s test, was used to evaluate the influence of overstory canopy and topographic variables on ecosystem functions and soil quality. Furthermore, structural equation modeling (SEM) was applied to disentangle the direct and indirect topographic variables effects on these functions. Results revealed significantly (P < 0.05) higher soil quality on northern slopes across all elevation classes. The highest soil quality (0.84 ± 0.01) was observed under closed canopies on northern mid-elevations, while the lowest (0.60 ± 0.03) occurred under open canopies on southern upper slopes. The greatest aboveground biomass (10.93 ± 0.3 t ha⁻¹) was recorded under closed canopies on northern upper slopes, whereas the lowest (8.39 ± 0.48 t ha⁻¹) was found under open canopies on southern mid-slopes. Soil carbon sequestration peaked under closed canopies on northern aspects, with the minimum value (7.01 ± 0.3 t ha⁻¹) detected under open canopies on southern upper slopes. SEM results indicated that the relationships among soil quality, carbon sequestration, and biomass varied with topographic position: on southern slopes, soil quality was primarily driven by carbon sequestration, whereas on northern slopes, aboveground biomass played a more prominent role. These findings underscore that ecosystem functions are shaped by both direct and indirect influences of biotic and abiotic factors, with biotic components exerting a relatively stronger effect. Moreover, a multi-functional assessment approach enhances our understanding of the intricate interconnections among ecosystem functions and the concurrent impacts of environmental drivers.