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Modulation of the commensal oral microbiota is a promising preventive or therapeutic strategy for oral health and can for instance be achieved by increasing the abundance and/or activity of certain species. This study evaluated whether 10 selected substrates could modulate in vitro multi-species oral biofilms towards a more health-associated state. These substrates were chosen based on the possibility that they could stimulate H2O2 production by certain commensal species and/or increase their abundance, as previously reported or as hypothesized based on known bacterial H2O2 pathways. Biofilms grown in presence of the substrates at a clinically relevant concentration of 1%(w/v) often showed increased abundances of commensal species and decreased abundances of periodontal pathogens. Furthermore, most biofilms also showed an altered metabolic profile. Effects on the expression of a selection of virulence genes were substrate-dependent, but often a decreased expression of certain genes could be observed. In conclusion, this study found that a selection of substrates chosen for their hypothesized beneficial effects on the commensal oral microbiota were able to modulate in vitro multi-species oral biofilms towards a more health-associated state. These modulatory effects were found to be substrate-dependent.