Herein, an innovative slow-release fertilizers (SRFs) were developed using a bio-based and waterborne polymeric coating containing starch-g-poly(styrene-co-butylacrylate) latex reinforced with natural char nanoparticles (NCNPs). Several SRF samples were prepared via coating the urea granules with the latex formulations containing different amounts of NCNPs, and their urea release rates were evaluated. The results showed that the presence of NCNPs nano-filler and decreasing the temperature could prolong the urea release time. The performances of the SRF samples were compared to urea granules and a commercial latex coating (SBR, poly(styrene-co-butyl acrylate)) on tomato production in the greenhouse. The results confirmed that NCNPs in coating formulation played an important role in improving plant growth and reducing N-release rate. The efficiencies of all the synthesized SRF samples were higher than the SBR-coated urea confirming the key-role of starch in the coating formulations. In sample containing 1 w% NCNPS (F13), total nitrogen percentage and nitrate content in the aerial parts of tomato plants were increased (21.1%) and decreased (42.1%) compared to the pristine urea, respectively. Particularly, application of F13 formulation could enhance the nitrogen use efficiency (NUE), nitrogen agronomic efficiency (NAE), and nitrogen apparent recovery fraction (NRF), 68.3%, 49.9%, and 29.7%, compared to the urea granules, respectively.