Using beneficial microorganisms along with sustainable strategies such as agronomic biofortification offers eco-friendly alternatives to combat climate change in ecosystems like dehesas. This study analyzes the combined effects of four wild Trichoderma spp. isolated from Extremadura, Spain (T. koningiopsis, two T. gamsii, and T. koningii, with negative and positive controls) and four Zn biofortification treatments (no Zn application; soil application of 5 mg of ZnSO4·7H2O per kg of soil, labeled soil Zn; two foliar applications of 5 mL 0.5% ZnSO4·7H2O, labeled foliar Zn; and soil + foliar combination, labeled SF) on Trifolium subterraneum performance. The combination of T. koningiopsis and T. gamsii with foliar Zn improved plant growth by up to 34.4%. Zinc accumulation was about 30% higher when T. gamsii and T. koningii were applied with SF, and their inoculation resulted in a 2.5-fold increase in ash. Trichoderma spp. affected nodulation differently; both T. gamsii inhibited nodulation by 24%, whereas neither T. koningiopsis nor T. koningii showed differences from the controls. These results highlight the potential of combining beneficial microorganisms with biofortification strategies to address nutrient deficiencies and improve agricultural sustainability. However, the complex interactions between both factors underscore the importance of strain selection and call for further research to optimize application strategies and elucidate underlying mechanisms.