<p>This study explored an eco-friendly, integrated strategy for managing root-knot nematode (RKN; <i>Meloidogyne incognita</i>) in greenhouse-grown tomato cv. Apache F₁. The strategy combined grafting (GR) onto resistant rootstocks (‘Estamino’: R₁ and ‘Fortamino’: R₂) with seed coating (SCB) using bacterial bioagent <i>Sporosarcina psychrophila</i> Sd4-11 (B₁) and <i>Streptomyces scabiei</i> Wb1n-4 (B₂). Grafted and ungrafted transplants, with or without seed coating, were cultivated in a naturally infested greenhouse during the 2022 and 2023 fall seasons using a randomized complete block factorial design. Comprehensive assessments were performed for host RKN-response, vegetative and reproductive performance, yield attributes, fruit quality, and metabolic activity, thereby addressing existing knowledge gaps regarding the combined efficacy of grafting and biocontrol strategies. The integrated GR-SCB approach significantly enhanced vegetative and reproductive growth, productivity, and metabolic activity, with markedly reducing RKN-infection. Analysis of variance revealed significant main and interaction (GR×SCB) effects across most measured traits, with seasonal and trait-specific variation. SCB most effectively suppressed RKN-satisfying response (number of galls and egg masses), whereas GR exerted the strongest influence on vegetative traits. The GR×SCB interaction contributed the highest proportion of variance in yield attributes (SS%: approximately 40–45%), confirming the synergistic potential. Principal component analysis (PCA) reduced 37 evaluated traits to three principal components explaining 97.06% of the total variance. PCA biplot results identified G-R₁/C-B₁ and G-R₁/C-B₂ as the most vigorous and RKN-tolerant combinations. Overall, integrating grafting with bioagent seed coating provides an effective, sustainable, and eco-friendly alternative to chemical nematicides for enhancing tomato productivity under protected cultivation.</p>