The present investigation was aimed to evaluate the impact of different nutrient sources viz., bio-fertilizer (effective microorganisms) with or without organic manure (Farmyard Manure) and inorganic fertilizer (NPK) on the quality characteristics of tomato. The pot experiment was conducted by combining 7 treatments in completely randomized design with 3 replications. The results revealed that nutrient sources significantly affected different quality parameters including; physicochemical (vitamin C, lycopene, total soluble solids and pericarp thickness); sensory (fruit color, fruit flavor and fruit firmness) and shelf life. It was concluded that bio-fertilizer integrated with Farmyard Manure emerged as better nutrient source over other treatments. Benefits of bio fertilizer application were more in the presence of Farmyard Manure on quality of tomato in comparison with NPK. No work has been previously published to study the effect of effective microorganisms on taste active components of vegetable or fruit crops, and their correlation with physicochemical attributes and shelf life. Data are provided for the researchers for further investigation.