Abstract: Tomato bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum, represents a major threat to tomato production. The pathogen employs multiple mechanisms to disrupt plant vascular systems, often leading to complete crop loss in susceptible cultivars. Moreover, R. solanacearum exhibits remarkable persistence in soil and plant debris, posing significant challenges for sustainable disease management. The increasing environmental concerns and pathogen resistance issues have imposed growing limitations on conventional control, such as chemical pesticides, thus necessitating the development of sustainable alternatives. In contrast, microbial fertilizers have emerged as a more promising green alternative, due to their environmental friendliness and remarkable soil improvement. As an important plant growth-promoting rhizobacterium (PGPR), Pseudomonas fluorescens demonstrates significant biocontrol potential through multiple mechanisms, including the production of over 10 antimicrobial secondary metabolites, competitive niche exclusion, and induction of systemic resistance. However, the practical application of PGPR has been significantly constrained by several technical challenges, including low survival rates, poor stability, and difficulties in large-scale production. Recent advances have demonstrated that the hydrogel encapsulation technology can overcome these limitations by providing physical protection and enabling controlled release of bacterial cells. Therefore, this study aims to develop a pH-responsive hydrogel bead system (SC11@APC) using sodium alginate (Alg), ε-poly-L-lysine (ε-PL), and calcium chloride (CaCl₂) for encapsulating the biocontrol strain Pseudomonas fluorescens SC11pLAFR-GFP (SC11). Its efficacy was also enhanced to serve as a biological control agent. Experimental results demonstrated that the 3% Alg/5% CaCl₂ cross-linked hydrogel formed a stable three-dimensional network structure, thus providing an optimal microenvironment for the SC11 encapsulation. The SC11@APC hydrogel beads effectively immobilized the SC11 strain within this porous matrix. Among them, the precisely engineered pore size prevented bacterial leakage to facilitate the antibacterial metabolite exchange. The encapsulation system maintained 61.2% bacterial viability after 21 days of storage, indicating the remarkable protective capacity. Live/dead staining assays further confirmed the significant inhibition of SC11@APC against Ralstonia solanacearum EP1. The hydrogel beads also exhibited the remarkable pH-responsive properties. The sustained release was regulated in the acidic rhizosphere environment, indicating the rapid responsiveness under pathogen-induced alkaline conditions. The SC11@APC hydrogel beads significantly promoted the tomato seedling growth. Three synergistic mechanisms were: (1) physical protection and controlled release of SC11 cells, (2) production and secretion of antimicrobial compounds for pathogen suppression, and (3) enhanced rhizosphere colonization and induction of plant systemic resistance. This multifunctional system was effectively maintained the bacterial viability for the dual benefits of disease control and growth promotion: (1) to achieve the complete (100%) disease suppression in treated plants, (2) to increase the seedling fresh and dry weights by 364% and 460%, respectively, compared with the infected controls, and (3) with the 29.6% and 33.3% improvements in biomass over SC11 suspension. The SC11@APC hydrogel has significant potential for sustainable agriculture. Material science and microbial ecology were synergistically combined to effectively address the soil-borne diseases. Further investigation is also required to evaluate its performance under complex field conditions for its growth-promoting mechanisms. Future research directions should focus on the optimization to develop more efficient and versatile microbial fertilizers, potentially extending applications to various high-value crops susceptible to vascular wilt diseases. The biodegradable composition, operational simplicity, and consistent laboratory performance can serve as a practical alternative for the diverse farming systems, from smallholder to large-scale agriculture. These findings can provide robust support to advance the biocontrol technologies and agricultural sustainability, according to the environmentally friendly design and effective disease prevention.