Conventional agriculture based on intensive agrochemical use threatens human health and worsens food insecurity, making multifunctional biological control agents a strategic priority. Entomopathogenic Metarhizium fungi combine insect pathogenicity with plant growth promotion. This study isolated native entomopathogenic fungi naturalized in La Araucanía, Chile, assessing in vitro growth-promoting traits and tomato (Solanum lycopersicum) physiology under greenhouse conditions. Twenty-five soil samples were collected from agroecological plots in La Araucanía; using Tenebrio molitor larvae as bait, and 59 fungal isolates were recovered using a monosporic culture. Isolates were evaluated in vitro for AlPO₄, phytic acid solubilization, indole-3-acetic acid and siderophore production. In total, 22 promising isolates were identified by ITS1–5.8S–ITS2 sequencing and Maximum Likelihood phylogenetics. Six isolates (MM23B, MM29C, G5X, MM26B, G9C, MM30D) were tested on tomato (S. lycopersicum) under a randomized greenhouse design (CRD), measuring growth, gas exchange, chlorophyll fluorescence, water use efficiency (WUE), photosynthetic pigments and lipid peroxidation. Highest AlPO₄ solubilization indices (3.24–3.14) were recorded for MM15D, MM17B, MM23D, and G5X. MM16B showed the highest phytic acid solubilization (40.5%) and MM24B the highest siderophore production (88.86%). Under greenhouse conditions, MM30D produced the highest net photosynthesis (131.24% above control), ΦPSII (0.2134), electron transport rate (56.00), and WUE (51.98), while G5X exhibited the highest stomatal conductance (0.39 mol H₂O m⁻² s⁻¹), transpiration (3.506), and maximum quantum yield (0.6784). All inoculated plants showed higher WUE than the control (19.43). Naturalized Metarhizium isolates from La Araucanía possess multifunctional traits supporting sustainable bioinput formulation.