Wheat (Triticum aestivum L.) sustains global caloric intake, but its productivity in Andean highlands is constrained by soil fertility and input reliance. This study represents one of the first field-based evaluations of biofertilizers under high-altitude, rainfed Andean conditions, addressing a major knowledge gap in low-input mountain agroecosystems. This study evaluated three seed-applied biofertilizers—Azospirillum brasilense, Trichoderma viride (Trichomax), and an anchovy (Engraulis ringens) based liquid biofertilizer, compared with an untreated control and a soil-test mineral fertilization benchmark in rainfed wheat (Triticum aestivum L.) cv. INIA 405 in the central Andes of Peru. A 5 × 5 Latin square design (25 plots) was established under farmer-realistic conditions. At physiological maturity (Zadoks 9.5), plant height, spike length, grains per spike, thousand-grain weight, test weight, root dry mass, and grain yield were recorded. Mineral fertilization achieved the highest yield (1.20 ± 0.79 t ha⁻¹), nearly doubling the control (0.60 ± 0.47 t ha⁻¹). Notably, A. brasilense delivered an intermediate yield of 0.90 ± 0.64 t ha⁻¹, representing a 50% increase over the control—accompanied by a marked rise in root dry mass. T. viride and the anchovy-based input yielded 0.85 ± 0.59 and 0.81 ± 0.59 t ha⁻¹, respectively. Grain physical quality remained stable across treatments (thousand-grain weight ≈ 42 g; test weight 68–75 kg hL⁻¹). Trait responses were complementary: root dry mass increased with mineral fertilization and A. brasilense, whereas spike length increased with mineral fertilization and the anchovy-based input. Overall, the evidence supports biofertilizers, particularly A. brasilense, as effective complements that enable partial fertilizer substitution within integrated nutrient-management strategies for sustainable wheat production in Andean rainfed systems.