Three-dimensional printed surgical guides increase the precision of orthodontic mini-implant placement. The purpose of this research was to investigate the effects of disinfection and of two types of autoclave sterilization on the mechanical properties of 3D printed surgical guides obtained via the SLA (stereolithography) and DLP (digital light processing) printing methods. A total of 96 standard specimens (48 SLA and 48 DLP) were printed to analyze the tensile and flexural properties of the materials. A total of 80 surgical guide (40 SLA and 40 DLP) specimens from each printing method were classified into four groups: CG (control group); G1, disinfected with 4% Gigasept (Gigasept Instru AF; Schülke & Mayer Gmbh, Norderstedt, Germany); G2, autoclave-sterilized (121 °C); and G3, autoclave-sterilized (134 °C). Significant differences in the maximum compressive load were determined between the groups comprising the DLP-(p < 0.001) and the SLA- (p < 0.001) printed surgical guides. Groups G2 (p = 0.001) and G3 (p = 0.029) showed significant parameter modifications compared with the CG. Disinfection with 4% Gigasept (Gigasept Instru AF; Schülke & Mayer Gmbh, Norderstedt, Germany) is suitable both for SLA- and DLP-printed surgical guides. Heat sterilization at both 121 °C and 134 °C modified the mechanical properties of the surgical guides.