Research on organic fertilizers are of crucial importance for sustainable production systems with high efficiency of natural resource use. The objective of this study was to evaluate organic sources of fertilization (boiled manure (BM), effective microorganism (EM) Bokashi, and Penergetic) for their effects on agronomic variables (fruit size and yield, total soluble solids) and on foliar powdery mildew severity of tomato (Solanum lycopersicum L.). The crops were grown during two cropping cycles in protected cultivation. The treatments were: Control (water only); 50 g per plant of EM Bokashi compost in two applications; Penergetic at 1.5 g L−1 applied to the substrate before planting or sprayed on the plants 14 days after transplanting; and BM at 2.5, 5.0, 7.5, and 10% concentrations (vol/vol) in water, via fertigation. Fruit production and quality were assessed. The effects of treatments on powdery mildew (Leveillula taurica Lév. G. Arnaud) were analyzed by using a diagrammatic scale. Bokashi, 10% BM, and Penergetic increased fruit production of the first three fruit trusses. Bokashi treatment increased tomato fruit diameter. The effects on fruit length and total soluble solids varied with each crop cycle. Powdery mildew severity increased with 10% BM, compared to the control. Both 10% BM and Penergetic presented similar fruit production to Bokashi and are good candidates as substitutes for Bokashi as organic fertilizers/amendments while maintaining tomato yield.