Environmentally friendly farming practices are gaining interest, and intercropping is a promising option to protect soil health, yet its effects on orchard microbiomes and functions remain underexplored. In this study, we assessed a 3-year intercropping assay of Capparis spinosa (D1) and Thymus hyemalis (D2) with almond and reduced tillage in a semi-arid Mediterranean orchard. Soil bacterial and fungal communities were profiled by metabarcoding (16S rRNA gene for bacteria/archaea and ITS region for fungi), functional potential was inferred from gene-abundance proxies and co-occurrence networks were constructed to evaluate alterations in microbial connectivity. Both intercropping treatments along with reduced tillage altered the soil microbial composition and enriched plant growth-promoting genera (e.g., Amycolatopsis, Bosea, Dyadobacter, Janthinobacterium, Leifsonia) and AMF (Glomeromycota), but effects were stronger in D2. Reduced tillage and intercropping with T. hyemalis increased the richness of less abundant bacteria, increased the abundance of functional potential linked to nitrogen fixation, cellulolysis, and fermentation. It also reconfigured co-occurrence networks toward higher connectivity with more module hubs - patterns consistent with greater functional stability. Overall, T. hyemalis intercropping with reduced tillage enhanced beneficial soil microbiota and higher functional potential than C. spinosa. Long-term monitoring is essential to ensure that the beneficial effects of intercropping persist and translate into real agronomic gains. For farmers, intercropping with thyme offers a valuable strategy to improve soil health and potential functionality while also generating additional income through products like essential oils-all without compromising almond orchard productivity. This dual benefit supports more sustainable and profitable farming in semi-arid regions.