This study examines the effects of different organic carrier materials, chicken manure, mill mud, and cow manure on the long-term viability and metabolite profiles of rhizobacterial strains Mesorhizobium sp. and Rhizobium sp. Over one year, growth curve analysis revealed significant differences in bacterial proliferation. Mill mud supported the most robust growth, with a doubling of 11 days, compared to chicken and cow manure, which exhibited growth saturation after five to eight months. Non-targeted 1H-NMR metabolite profiling revealed distinct sugar and amino acid profiles across carriers. Mill mud exhibited a broader range of sugars, including sucrose, maltose, and mannose, while chicken and cow manure primarily contained monosaccharides like glucose, xylose, and mannitol. Amino acids such as lysine and glutamate were higher in chicken manure, followed by cow manure and mill mud. Plant growth-promoting metabolites were detected in all carriers, with Mesorhizobium sp. and Rhizobium sp. enhancing their production by up to 200% in mill mud and cow manure. Both bacterial strains utilized sugars from the carriers, with Mesorhizobium sp. showing more consistent sugar metabolism. These findings suggest that mill mud is an effective carrier for sustaining rhizobacterial viability and enhancing metabolite production, benefiting biofertilizer formulations and soil health.