The need to produce crop in an eco-friendly manner using organic agriculture that avoids using synthetic chemicals and fertilizers become imperative as a way of protecting man, other beneficial organisms from chemical toxicity and environmental pollution. This experiment was, therefore, conducted in screen house during two consecutive years of 2017 and 2018 at Teaching and Research Farm, Landmark University Omuaran, Kwara State, Nigeria to investigate the differential response of five tomato cultivars infested with root knot nematode under both organic and inorganic fertilizers application in order to determine the most resistant cultivars with the view of recommending such cultivar(s) to farmers, who may wish to go into large scale production of the crop in Southern Guinea Savannah ecological zone, Nigeria. Poultry manure was used as soil amendment and incorporated into the soil at the rate of 1.42 t/ha, while NPK was applied at the rate 266 kg/ha. The experimental design was 5 × 2 × 2 factorial experiment, made up of five tomato cultivars, (Tropimech, Rio Grande, Dan hausa, Igede local and Omuaran local) with two manure types (Poultry and NPK fertilizer) and two media application (inoculated and uninoculated). Data were taken on Plant height, number of leaves, stem girth at 6, 8, 10 and 12 weeks after planting, number of flowers and number of days to 100% flowering, number of fruit, fruit weight (yield component), soil nematode population and root gall index. The results of the experiment showed that poultry manure recorded the highest vegetative growth (119.07 g/plant) and tomato yield (133.42 g/plant) even under high level of nematode infestation. The cultivar Igede local showed the highest level of nematode infection tolerance despite the high level of M. incognita infestation. It is the highest yielding among the tested cultivars under organic amendment condition and the most tolerant to nematode infection. Igede local is, therefore, recommended for use as seed in all nematode endemic soil.