Organic fertilizers and microbial biofertilizers are now widely recognized to effectively complement traditional mineral fertilizers for plant growth. The present study shows that bio-organic fertilizers can be enhanced by the addition of functional plant-growth-promoting rhizobacteria (PGPR) that provide additional benefits to plants. We hypothesized that not all beneficial soil bacteria are functional in different farm soils and plant varieties; hence, the most effective PGPR that are suitable to each farm’s individual cropping conditions were selected. Five different field soils and their respective crops were tested for compatibility with six microbial biofertilizers (including three new bacterial strains) to supplement a commercially available bio-organic fertilizer. In pot trials with lucerne plants, four out of the six microbial treatments led to significant (p < 0.05) growth promotion benefits (up to 79.8% more leaves and dry weight) compared to mock-treated or bio-organic fertilizer-only-treated control plants. A trial with industrial hemp demonstrated that compatibility with PGPR occurs in a cultivar-specific manner, leading to growth promotion ranging from −3.4% to 68.9%, with each cultivar displaying a preference for a different PGPR. Finally, pot trials with Rhodes grass and two different soils demonstrated high yield increases compared to control plants, with Bacillus amyloliquefaciens 33YE being most effective for one soil and Bacillus velezensis UQ9000N/Pseudomonas lini SMX2 for the other soil. Yield advantages reduced after several cuts of grass, but a repeat biofertilizer treatment at 69 days after the initial treatment restored high yield advantages, with the same PGPR again being most effective. These results demonstrate the importance of customization of microbial inoculants to identify the most compatible PGPR–cultivar–soil interaction. The customization of microbial biofertilizers to soils and plant cultivars, combined with complementary fertilizer applications, can potentially lead to more reliable and more sustainable agricultural practices.