BC204 is a citrus‐based plant extract applied as a plant biostimulant on a variety of plant species in South Africa, China, and Australia. Although there are reports that it elicits physiological responses such as an increase in crop yield, abiotic and biotic stress tolerance, and fruit quality, no molecular data are available to explain the specific mechanisms underlying these effects. In this study, an RNA sequencing approach was adopted to elucidate the effects of BC204 at the molecular level in Arabidopsis thaliana and Solanum lycopersicum. BC204, applied via either a 0.01% (v/v) soil drench to A. thaliana or a 0.05% (v/v) foliar spray to S. lycopersicum, stimulated above‐ground biomass production whilst eliciting a large change in gene expression levels across several primary and secondary biochemical pathways in shoot tissues. Of the entire transcriptomic profile examined, 8.212% of genes were significantly differentially expressed between the treated and control groups in A. thaliana and 18.059% of genes for S. lycopersicum. Most notably, genes involved in photosynthesis, several aspects of cell wall biogenesis, remodeling and restructuring, carbohydrate metabolism, signaling, stress, and secondary metabolism were upregulated, which could explain the observed increase in plant growth. Little correlation in types of gene and pathway induction was observed between the two model organisms. Genes related to transcription and RNA regulation were both strongly up‐ and downregulated, which suggests that BC204 plays a role in inducing and suppressing several pathways. This novel study provides valuable information to be used as a starting point for targeted future research and identifying new targets for enhanced plant growth and vigor.