Tree intercropping systems with leguminous cover crops and aromatic plants may provide sustainable yields, which could be improved by beneficial microbes (BMs) and zeolite, while their effects on young tree growth remain unclear. We tested whether such systems enhance early growth in young carob trees compared with conservation tillage (TLG) trees growing under rainfed semi-arid conditions. Intercropping included carobs with (i) Lathyrus ochrus, Trifolium squarrosum, and Lens culinaris combined (CC-System), (ii) Thymbra capitata planted between legumes (CCT-System), and soil amended with (iii) BM (Micosat-F-Olivo) and zeolite. All systems outperformed TLG in annual tree height increase with the CC-System excelling (TLG +13%, CC-System +42%; p < 0.05). The CC-System also significantly outpaced TLG in stem thickening (TLG 62%, CC-System 167%; p < 0.01) with BM and/or zeolite also appearing as beneficial. Improved performance was related to significantly higher dry season soil moisture, while a high L. ochrus abundance reduced thyme survival (p < 0.01). The CCT-System was also found to be less capable in weed suppression during a wet year. Thus, applying our legume intercropping system (with BM/zeolite) represents an effective nature-based solution for enhancing young carob tree growth under rainfed conditions, while adding thyme may somewhat trade productivity for biodiversity and associated ecosystem services.