Benzo[a]pyrene (BaP) is a highly carcinogenic persistent organic pollutant, and biostimulation is an effective strategy to enhance its degradation. This study utilized Bacillus subtilis MSC4 as a BaP-degrading bacterium to investigate the effects of two different fermentation waste liquids as stimulants on BaP degradation. The mechanisms were analyzed and compared at both the cellular and molecular levels. The results showed that the stimulation percentages of yeast Yarrowia lipolytica extracellular metabolites (YEMs) and Lactobacillus plantarum fermentation waste solution (LPS) on the biodegradation of BaP reached 52.8% and 63.4%, respectively, compared to B treatment without biostimulant. Physiological analyses showed that both stimulants repaired cell morphology, more than doubled bacterial biomass, increased EPS secretion, enhanced bacterial activity, and significantly reduced oxidative stress by lowering ROS levels to 75-78% of those in the BaP-stressed group, allowing for repair of oxidative damage. Transcriptomic analysis indicated that both stimulants upregulated pathways related to central carbon metabolism, enhancing cell proliferation and energy supply. Additionally, YEMs promoted electron transport and BaP transmembrane transport and upregulated the synthesis of various monooxygenases, while LPS induced the upregulation of genes encoding quercetin dioxygenase and played a more active role in biofilm formation and enhancing BaP bioavailability. This study reveals the shared and distinct mechanisms by which YEMs and LPS enhance BaP biodegradation, providing theoretical guidance for the application of YEMs and LPS in the bioremediation of BaP-contaminated environments.