The experiment was conducted on a private farm at Northern Elselait Scheme, Khartoum State, Sudan to study the effect of fertilization method, soil type, and microorganism application on the growth and yield of tomatoes crop op under greenhouse conditions. Silt soil and two types of fertilizing units (injector and by-pass) were used for applying effective microorganisms (EM) in two levels (0 and 12 L/ha), at fortnight intervals after 45 days to 90 days from planting. A split-plot design was used with three replications. The data collected were: plant height, number of leaves, stem diameter, number of flowers, number of fruits, and weight of fruits per plant. . The production indicators showed that tomato crop agronomic parameters were significantly (P ≤ 0.05) affected by the method of fertigation and application of effective microorganisms. A mean yield of 5.4 tons per hectare of plants grown on silt soil and fertilized with effective microorganisms (EM) using an injector fertilizing unit,  when fertilization  was done by a by-pass fertilizer system applying effective microorganisms (EM) gave a  yield of 4.6 ton/ha and yield ton per hectare of silt soil fertilized by injector fertilizer with non-applied effective microorganisms (EM0) was 7.3 ton/ha, while with silt soil fertilized by a by-pass fertilizer unit with non-applied effective microorganisms (EM0) it was 5.5 ton/ha.