Agroforestry systems have been compared to agricultural and forestry alternatives, providing a land-use solution for additional environmental benefits while maintaining similar levels of productivity. However, there is scarce research assessing such patterns across a pan-European scale using a common methodology. This study aims to improve our understanding of the role of trees in three different regulating ecosystem services—(1) soil erosion, (2) nitrate leaching and (3) carbon sequestration—in traditional and innovative agroforestry systems in Europe through a consistent modeling approach. The systems’ assessment spans environmentally from the Mediterranean environmental region in Portugal to the Continental environmental region in Switzerland and Germany to the Atlantic environmental region in the United Kingdom. Modeled tree densities were compared in the different land-use alternatives, ranging from zero (agriculture with only crops or pasture) to forestry (only trees). The methodology included the use of a biophysical model (Yield-SAFE) where the quantification of the environmental benefits was integrated. Results show a consistent improvement of regulating ecosystem services can be expected when introducing trees in the farming landscapes in different environmental regions in Europe. For all the systems, the forestry alternatives presented the best results in terms of a decrease in soil erosion of 51% (±29), a decrease of nearly all the nitrate leaching (98% ± 1) and an increase in the carbon sequestration of up to 238 Mg C ha–1 (±140). However, these alternatives are limited in the variety of food, energy and/or materials provided. On the other hand, from an arable or purepasture alternative starting point, an increase in agroforestry tree density could also be associated with a decrease in soil erosion of up to 25% (±17), a decrease in nitrates leached of up to 52% (±34) and an increase in the carbon sequestered of 163 Mg C ha–1 (±128) while at the same time ensuring the same levels of biomass growth and an increase in product diversification.