Driven by ecological awareness on excessive use of agrochemicals, research and industry have turned to plant growth promoting rhizobacteria (PGPR) that exhibit significant plant growth promoting and/or biocontrol activities. Most adopted selection procedures for PGPR exclusively consist of the in vitro isolation and selection of bacterial strains with desired agronomic traits, which are only tested on a host plant in the last screening steps. As rhizosphere competence and activity are not accounted for in the initial in vitro selection, promising candidates often fail to perform in planta. Therefore, we developed an in planta enrichment platform coupled to a phenotyping platform which simultaneously selects for biostimulant traits and rhizosphere competence. The platform was utilized to select for phosphate solubilizing bacteria (PSB) on maize (Zea mays L.). As maize exhibits phosphorous deficiency through the accumulation of anthocyanin, we calculated the modified Anthocyanin Reflectance Index (mARI) through the phenotyping platform encompassing an automated multispectral camera, enabling a non-destructive assessment of the phosphorous deficiency status of maize plants. Through a cyclic in planta inoculation approach under phosphorous limiting conditions, several microbial consortia were generated. When inoculated onto maize plants grown in the presence of insoluble phosphorous, some consortia induced a comparable anthocyanin phenotype and phosphorous content to maize plants grown on full nutrient solution. This platform has shown the potential to effectively generate bacterial biostimulants, from which now individual strains can be isolated for further assessment. Currently we are expanding the use of the phenotyping platform to other nutrient deficiencies such as nitrogen, zinc, manganese and iron, and exploring its use for the selection of biocontrol strains against plant pathogens.