The banana plant holds significant importance in Indonesia and other Southeast Asian countries. Recently, the intensive use of biological fertilizers derived from soil microbes in horticulture productions has been reported for various beneficial reasons. These include improved nutrient availability, enhanced soil structure, disease suppression, increased plant stress tolerance, and environmental sustainability. This study examines the expression of nutrient uptake-related genes following applying a soil consortium consisting of Lysinibacillus xylanilyticus and Bacillus pseudomycoides. The banana plants were subjected to four 100 ml bacterial consortium suspension applications. Morphological and physiological observations were conducted in a greenhouse, while eight genes’ expression levels were assessed using semi-quantitative real-time PCR. The research employed a design with two treatments: control and application of the consortium bacteria; each replicated 10 times. The findings revealed that the treated plants exhibited the highest increase in leaf length during 40 days. Additionally, the plants treated with the bacterial consortium demonstrated increased gene expression associated with efficient phosphate and nitrogen uptake, specifically in Ma01_g01890, Ma03_g26260, WRKY26, WRKY31, and WRKY33 genes, after fourteen days of bacterial application. Consequently, this consortium can be employed as a biofertilizer for plants.