The main objective of the present study was to determine how treatment with low-temperature plasma (LTP) at different exposure times affects cariogenic biofilms of single and multiple species formed by C. albicans, L. casei, and S. mutans on hydroxyapatite discs. Biofilms were treated with LTP-argon at a 10 mm distance for 30 s, 60 s, and 120 s. Chlorhexidine solution (0.12%) and NaCl (0.89%) were used as positive and negative controls, respectively. Argon flow was also used as gas flow control. Colony-forming units (CFU) recovery and confocal laser scanning microscopy (CLSM) were used to analyze biofilm viability. LTP reduced multispecies biofilms viability (log10 CFU/mL) in all the treated samples (p < 0.0001). For single-species biofilms, a significant reduction in all exposure times was observed for L. casei (p < 0.0001). For C. albicans biofilms, there was a significant decrease in LTP treatment when applied for 60 and 120 s when compared to positive and negative controls (p < 0.0001). LTP is a potential mechanism in the treatment of dental caries, by being an effective anti-biofilm therapy of both single and multispecies cariogenic biofilms.