This study explored the influence of cell‐free spent media prepared from Aggregatibacter actinomycetemcomitans LuxS mutant (Aa‐LuxS), its wild type strain (Aa‐WT), and the laboratory strain (Aa‐Y4), on the interaction between Candida albicans and Streptococcus mutans while growing in co‐species biofilm for 48 h. By analyzing the results of crystal violet staining, [3‐(4,5‐dimethyl‐2‐thiazolyl)‐2,5‐diphenyl‐2H‐tetrazolium bromide] (MTT) assays, and quantitative real‐time polymerase chain reaction (qPCR), we found that the presence of Aa‐LuxS in treated biofilms did not affect biofilm development, while added Aa‐WT or Aa‐Y4 resulted in a significant decrease in both biofilm mass and the number of cells. The inhibitory effect of Aa‐WT or Aa‐Y4 was not dependent on the protein concentration in the spent media tested (1 and 10%). Gene transcription analyses indicated that Aa‐WT/Aa‐Y4 exhibits comparable inhibitory effects on the expression of hyphal‐associated genes (ALS3 and HWP1), but not on the expression of YWP1, which encodes a yeast form of C. albicans. In contrast, except for gtfD, the expression of S. mutans gtfB/C genes encoding glucosyltransferase was not affected in Aa‐WT and Aa‐Y4 treated biofilms compared to the levels found in Aa‐LuxS treated biofilms. Our results indicate that AI‐2‐containing spent media derived from Aa can reduce biofilm biomass without significantly inhibiting the survival rate of S. mutans.