Soil salinity limits agriculture in arid and semi-arid regions where large-scale leaching is impractical. Biopolymer-based microencapsulation for bioinoculant delivery offers a sustainable approach to rehabilitating saline soils and improving crop performance. We evaluated twelve halotolerant plant growth-promoting rhizobacteria (PGPB ) applied as free cells and chitosan–starch microcapsules, with or without organic liquid fertilizer (OLF), to enhance safflower ( Carthamus tinctorius L.) growth and soil desalination. Greenhouse factorial trials (three replications) assessed morphological, physiological, and biochemical plant traits, and soil Na⁺, K⁺, Ca²⁺, and electrical conductivity (EC). Data were analyzed using factorial ANOVA (LSD, p < 0.05) in SAS v9.4, with multivariate relationships explored by PCA in Python (scikit-learn v1.4.0). Microencapsulation enhanced PGPB viability, colonization, and function. Integrator strains ( Rhizobium sp., Agrobacterium tumefaciens, Rhizobium radiobacter ) reduced EC by up to ∼51%. Specialist strains (Pseudomonas fluorescens, Micrococcus luteus ) increased targeted metabolites, while persistent strains ( Bacillus licheniformis, Kushneria sp.) maintained remediation. The chitosan–starch carrier provided mechanical protection, enzyme stabilization, and promoted exopolysaccharide-mediated soil aggregation. Combining diverse PGPB types with biopolymer encapsulation and organic amendments offers a scalable, low-impact solution for salinity mitigation. These greenhouse findings demonstrate the potential of microencapsulated halophilic PGPB for sustainable saline soil management, pending further field validation and biosafety assessment.