Objective: This study was conducted to investigate the effect of effective microorganisms (EM), farm yard manure and nitrogen on yield and quality of tomato. Methodology: A factorial experiment was carried out at the Research Farm of Gezira (Medani), Shendi and Hudieba in 2009/10. The factors studied were N (0 and 2N as urea), farm yard manure (0 and 10 t/ha) and EM (-or +). The treatments were arranged in RCBD with four replicates. The data collected involved tomato marketable yield and quality in term of fruit firmness and total soluble solids. Results: The results revealed that 2N application significantly increased the yield at Medani and Hudieb but not at Shendi. EM improved the yield of the control and manure by 12-31 and 7-18%, respectively, but these increments were not significant. The highest yield of tomato was recorded at Medani and Hudieba in manure integrated with 2N. However, the yield obtained by the use of manure alone was not significantly different from that of manure with 2N but significantly the highest among the other combinations at Shendi. Each of N and manure significantly improved the firmness of tomato at Medani. Hence, manure applied separately or integrated with 2N could be used for the organic production of tomato and yield maximization, respectively, at Medani and Hudieba. Separate use of manure was suggested for both yield maximization and organic tomato production at Shendi. Conclusion: It could be concluded that the integrated use of manure and nitrogen fertilizer significantly resulted in the highest tomato yield when the total soil N is low as in Medani and Hudieba. Application of manure alone showed comparable yield to that of combined manure and 2N but significantly higher than that of 2N when the total soil N is high as in Shendi.