Purpose: This study was designed to investigate the in vitro effects of geraniol (GE) and thymoquinone (TQ) on Candida biofilms on denture acrylic and any accompanying changes in acrylic surface roughness or color. Methods: The susceptibility of Candida species to GE and TQ was determined using the broth microdilution method and time-kill assay. A minimum biofilm eradication concentration (MBEC) assay was performed using 7-day Candida biofilms grown on denture acrylic. Results: The minimum inhibitory concentration (MIC) of GE and TQ for Candida spp. was 256 and 32 µg/mL, respectively. The Candida strain complete kill rates for GE and TQ at 5-fold MIC were determined after 1 h of incubation. At 5-fold MIC, GE and TQ inhibited the preformed biofilm activity (MBEC80) of all Candida strains on denture acrylic by more than 80% after treatment for 3 h. At sub-MIC levels, GE and TQ prevented the development of C. albicans and C. tropicalis hyphae. SEM images demonstrated that GE and TQ damaged the fungal cell membrane and induced cell lysis. On the other hand, GE and TQ at 10-fold MIC did not alter the surface roughness or color of the denture acrylic. Conclusion: GE and TQ are interesting natural substances that could be developed as promising disinfectants for removable dentures.