Background: Vinegar has been recognized as an effective antimicrobial agent for long. This study intended to elucidate the effect of commercially available vinegar on in situ pellicle formation and existing 24-h biofilms. Methods: In situ biofilm formation took place on bovine enamel slabs mounted in individual splints and exposed intraorally over 3 min and 24 h, respectively. After 5 s rinsing with vinegar, all samples were analyzed via fluorescence microscopy (FM), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). In addition, salivary samples were collected and analyzed via FM. Samples with water rinsing served as controls. Results: Vinegar caused destruction of the pellicle. Compared to the control group, vinegar rinsing reduced the outer globular layer of the pellicle (p < 0.001), and resulted in formation of subsurface pellicle. Also, vinegar rinsing could reduce bacterial viability and disrupt the 24-h biofilm. Total bacteria amount of saliva samples decreased remarkably (p < 0.001) after vinegar rinsing within 30 min. Reduction of bacterial viability was observed even 120 min after vinegar rinsing in both biofilm and saliva sample (p < 0.001). Conclusion: This in situ study reveals that rinsing with vinegar for only 5 s alters the pellicle layer resulting in subsurface pellicle formation. Furthermore, vinegar rinsing will destruct mature (24-h) biofilms, and significantly reduce the viability of planktonic microbes in saliva, thereby decreasing biofilm formation.