The existing trade-off between agricultural production and ecosystem services is widening with the intensification of agricultural systems. In this context, diversification can play a crucial role in enhancing agroecosystem multifunctionality, and in orchard systems it can also be achieved through the management of inter-row spaces via the ecological functions provided by sown and resident vegetation. Nowadays its contribution is not recognised. The study aims to compare the temporal dynamics of four cover crop mixes present in the inter-row spaces and assess their ecological functions using the Vegetation-based Ecological Functions Sustainability Index, and evaluate the relative influence of management, season, and year on cover crop performance. Total and relative coverage and species number were collected from 2022 to 2024. Non-metric multidimensional scaling analysis showed that vegetation composition varied across treatments, and cover crop management shaped plant community structure. It highlighted that the strongest difference was the contrast between grass cover (r = −0.95) and bare soil (r = 0.91). Permutational Multivariate Analysis of Variance on ecological functions indicated that sampling year (R² = 0.1822, F = 8.4874, p < 0.001). and season (R² = 0.1280, F = 5.9659, p < 0.001) had a significant impact on vegetation cover. Moreover, biodiversity effects hinge primarily on the ecological functions performed by species, rather than on their number. Overall, these findings highlight that the ecological contribution of inter-row vegetation depends more on the functional traits expressed by plant communities than on species richness alone. Furthermore, year and season strongly influence the dynamics of cover crops and resident vegetation, making multi-year monitoring essential to determine their persistence and the ecological functions they perform.