Recent in vivo studies by our group revealed that some proteins increased acid-resistant proteins in the acquired enamel pellicle (AEP) after challenges with citric acid. This makes the use of these proteins to control the dental biofilm particularly attractive. Thus, the present proof-of-concept study was designed to pave the way for the use of some proteins to control caries through acquired pellicle and biofilm engineering. Combining in vivo and in vitro protocols and employing state-of-the-art OMICS techniques, our aim was to evaluate whether proteins can alter the proteome of the AEP and consequently interfere with initial bacterial colonization and enamel demineralization.