OBJECTIVES: This study compares the effects of thermoplastic polyurethane (TPU) and polyethylene terephthalate glycol (PETG) aligners on the oral microbiome and salivary pH during orthodontic treatment. MATERIALS AND METHODS: Ten participants wore TPU and PETG aligners for 24 h. At five time points (1 min, 4, 8, 12, and 24 h), saliva was collected for pH analysis, and microbial samples were taken from both aligner and supragingival plaque surfaces for 16S rRNA sequencing. Statistical analyses included repeated Measures ANOVA for pH, Kruskal-Wallis test for alpha diversity, PERMANOVA for beta diversity, and two-way ANOVA for microbial composition. RESULTS: In Group PETG, salivary pH significantly decreased from T0 to T4 (p < 0.05). No significant changes in alpha or beta microbiota diversity were observed in either group. Microbial shifts in supragingival plaque microbiomes were detected at T8 in Group PETG, while in Group TPU, these changes became evident between T12 and T24. In aligner microbiomes, Group TPU showed significant reductions in Veillonella, Actinomyces, and Fusobacterium at T24 (p < 0.05). In contrast, Group PETG exhibited significant increases in Streptococcus from T4 to T24 (p < 0.05) and Fusobacterium from T0 to T4 (p < 0.05), followed by a decline from T4 to T24 (p < 0.01). CONCLUSIONS: PETG aligners caused significant reductions in salivary pH at T4 and triggered pronounced fluctuations at T8 in supragingival plaque microbiomes. TPU aligners caused a delayed decline in salivary pH between T8 and T12 and drove distinct structural shifts during prolonged wear from T12 to T24. CLINICAL RELEVANCE: Material choice based on microbial impact highlights the need for personalized aligner materials and cleaning cycles.