As a result of the growing concerns about the adverse effect of chemicals on the environment, agricultural practices involving organic and environmental-friendly compounds are gaining acceptance globally. Tomatoes remain one of the most popular and widely grown vegetable crops. However, their growth requires a high supplement of nitrogen–phosphorus–potassium (NPK) fertilizer. The effectiveness of vermicompost leachate (VCL) as a potential replacement for the three elements (N, P, and K) during the growth of greenhouse tomatoes was evaluated. Morphological appearance of the tomato seedlings was remarkably enhanced when Hoagland’s nutrient solution (50%) was supplemented with VCL (1:10 v/v). In the absence of both P and K, the addition of VCL significantly (P = 0.05) increased various growth parameters such as shoot length, leaf number as well as shoot and root fresh weight compared with the control tomato seedlings. The detrimental effect of N deficiency on the growth of tomato seedlings was not alleviated with the addition of VCL to the nutrient solution. The photosynthetic pigment content in P-deficient and VCL-supplemented tomato seedlings was significantly higher than the untreated control. The presence of VCL alleviated the detrimental effects caused by deficiency of P and K during the growth of the tomato seedlings. Overall, the use of VCL was beneficial with either complete nutrient solution or in the absence of P and K. Findings of this study suggest that VCL could serve as a potential substitute for P and K deficiency.