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Because hydroponic operations in the United States can be certified as organic, and because the price of chemical fertilizers has increased, there is an increasing interest in using organic fertilizers and beneficial microorganisms for controlled-environment agriculture. However, there is a scarcity of information regarding their effectiveness and application methodologies. We investigated the effects of inoculating Azospirillum brasilense and Rhizophagus intraradices and using organic fertilizers on growing lettuce (Lactuca sativa ‘Cherokee’) and tomato (Solanum lycopersicum ‘Red Robin’) young plants in an indoor vertical farm. Seeds were sown in rockwool substrate, with A. brasilense (1.05 × 108 colony-forming units⋅L−1) or R. intraradices (580 propagules⋅L−1) applied weekly via subirrigation. Seedlings received chemical fertilizer, organic fertilizer derived from corn steep liquor and fermented fish by-products, and food waste-derived organic fertilizer at 100 ppm total nitrogen every 2 or 3 days. They were grown indoors at 23 °C under light-emitting diode lighting at a photosynthetic photon flux density of 200 μmol⋅m−2⋅s−1 with an 18-hour photoperiod. Lettuce under organic fertilizers had 75% lower shoot fresh mass and 64% less shoot dry mass compared with lettuce under chemical fertilizer. Similarly, tomato seedlings with organic fertilizers had fewer leaves, 75% less shoot fresh mass, and 67% less shoot dry mass. In both lettuce and tomato, the macronutrient and micronutrient concentrations in plant tissues were generally similar regardless of fertilizer treatments, but nitrogen use efficiency and nitrogen uptake efficiency were lower under organic fertilizers compared with those under chemical fertilizer. The inoculation of A. brasilense or R. intraradices showed limited effects on plant nutrient uptake, nutrient concentrations, and seedling growth in both lettuce and tomato. Further research is necessary to optimize application methods for organic fertilizers and beneficial microorganisms to fully harness the benefits of sustainable alternative fertilizers in soilless and hydroponic crop production. [ABSTRACT FROM AUTHOR]