The modern agriculture is working on introducing new generation of fertilizers that apt to slow down the nutrients release to be more in synchrony with plant’s need throughout growth season, enhance fertilizer performance, and decrease nutrient losses into the environment. The aim of this research was to develop an advanced NPK slow-release fertilizer (SRF) and investigate its effect on yield, nutritional and morphological responses of tomato plant (Lycopersicon esculentumMill.) as a model crop. To this goal, three water-based bio-polymeric formulations including starch-g-poly (acrylic acid-co-acrylamide) nanocomposite hydrogel, starch-g-poly(styrene-co-butylacrylate) latex, and carnauba wax emulsion were synthesized and used for production of NPK-SRF samples. Different samples of coated fertilizers (urea, potassium sulfate, and superphosphate granules) were prepared using different ratios of latex and wax emulsion, and for phosphorus and potash (R-treatment). Moreover, some of coated fertilizers (15 and 30 wt.%) was replaced with nanocomposite hydrogel containing fertilizers, named D and H treatments, respectively. The effect of SRF samples were compared with commercial fertilizers (NPK treatment) and a commercial SRF (T treatment), on the growth of tomato in the greenhouse, at two different levels (100 and 60). The efficiency of all the synthesized formulations were higher than NPK and T treatments, and among them, H100 significantly improved the morphological and physiological characteristics of tomato. For instance, amount of residual elements (nitrogen, phosphorus and potassium) as well as micro elements of calcium, iron and zinc in tomato cultivation bed and accordingly the uptake of these elements in the roots, aerial parts and fruits were increased in the R, H, and D treatments. The highest yield (1671.54 g), highest agricultural agronomy efficiency of fertilizer, and the highest dry matter percentage (9.52%) were obtained in H100. The highest amount of lycopene, antioxidant capacity and vitamin C was also observed in H100. Nitrate accumulation in tomato fruit in the synthesized SRF samples were decreased significantly compared to NPK100, and the lowest amount was observed in H100, which was 55.24% less than NPK100. Accordingly, it is suggested that combination of natural-based nanocomposite hydrogels along with coating latexes and wax emulsions can be a successful method to synthesize efficient NPK-SRF formulations for improvement of crop growth and quality.