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 similar 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.