Beneficial and probiotic bacteria play an important role in conferring the immunity of their hosts against a wide range of bacterial, viral, and fungal diseases. B. subtilis is a bacterium that protects the plant from various pathogens due to its capacity to produce an extensive repertoire of antibiotics. At the same time, the plant microbiome is a highly competitive niche, with multiple microbial species competing for space and resources, a competition that can be determined by the antagonistic potential of each microbiome member. Therefore, regulating antibiotic production in the rhizosphere is of great significance to eliminate pathogens and to establish beneficial host-associated communities. In this work, we used Bacillus subtilis as a model to investigate the role of plant colonization in antibiotic production. Flow cytometry and Image-stream analysis supported the notion that A. thaliana specifically induced the transcription of the biosynthetic clusters for the non-ribosomal peptides surfactin, bacilysin and plipastatin and the polyketide bacillaene. Our results can be translated to improve the performance and competitiveness of beneficial members of the plant microbiome.