Background: The aim of this study is to evaluate the effect of self-assembling peptide (SAP) P11-4 on the Streptococcus mutans American Type Culture Collection (ATCC) 10449, Lactobacillus casei ATCC 11578 and Candida albicans ATCC 60193 and to compare the antibacterial and antifungal activity with different remineralisation agents. Methods: This in-vitro microbiological study was performed with five independent groups (G1. Chlorhexidine Gel (Best Dental, Istanbul, Turkey), G2. Profluorid Varnish® (VOCO GmbH, Cuxhaven, Germany), G3. Curodont™ Protect (Credentis AG, Windisch, Switzerland), G4. Tooth Mousse™ (GC Corporation, Tokyo, Japan) and G5. MI Paste Plus (GC Corporation, Tokyo, Japan)). The antimicrobial activities of the samples were evaluated according to 24-hour time kill assay against S. mutans, L. casei and C. albicans. Results: The control, Group 1—Chlorhexidine gel, had the strongest antibacterial activity against all of the tested microorganisms. The results showed that Group 4—Tooth Mousse™ was the most effective remineralization agent with the best antimicrobial activity against S. mutans and C. albicans, followed behind respectively with Group 5—MI Paste Plus, Group 3—Curodont™ Protect, and Group 2—Profluorid Varnish®. Group 5—MI Paste Plus demonstrated the most effective antibacterial activity against L. casei. Group 4—Tooth Mousse™, Group 2—Profluorid Varnish®, and Group 3—Curodont™ Protect were afterwards in order. Conclusions: SAP P11-4 can be used as an antimicrobial agent to prevent opportunistic fungal infections as well as to prevent and halt the progression of incipient lesions.