Controlled environment agriculture is becoming increasingly important in a world where climate change has made conventional farming uncertain. Hydroponic agriculture is an attractive option due to its efficient use of nutrients and water, but is still not quite sustainable. Organic hydroponics is a possible solution to this barrier. This experiment tested the effectiveness of organic fertilizer with and without vermicompost extract (VCE) on hydroponic spinach production when compared to a conventional fertilizer control. It was hypothesized that the vermicompost would promote growth of a microbial community, including nitrifying bacteria, that would be beneficial to plant growth. Growth chamber experiments using hydroponic ponds were conducted over three consecutive harvests. Yields increased over time in organic treatments with vermicompost extract, and the Organic + 10% VCE treatment was comparable to the control by the third harvest. The Organic + 5% VCE treatment had a similar positive trend over time but overall had lower yields than the control. Organic treatments without the vermicompost additive had significantly lower yields than the control throughout the experiment. Nitrogen analysis of the nutrient solution, temporal pH data, and rhizobiome microbial assays indicated the presence of a beneficial nitrifying community in organic treatments with the vermicompost extract. These findings show that vermicompost extract may help to make organic hydroponics a viable industry through encouraging the development of a beneficial microbial community in the system.