Background: Calcium hydroxide is a routinely used material for root canal disinfection during root canal treatment. Natural products have great potential in terms of their antibacterial effects. This study aimed to establish an effective alternative intracanal medicament using Origanum dubium (O. dubium) and Mentha spicata (M. spicata) essential oils. Materials and Methods: O. dubium and M. spicata, collected from Lefke, Cyprus, were separately subjected to hydrodistillation. The obtained essential oil compositions were analysed simultaneously by gas chromatography (GC) and gas chromatography/mass spectrometry (GC-MS). The compositions were then divided into groups and mixed with calcium hydroxide at a 1:1 concentration; after that, the pastes were tested on Enterococcus faecalis (E. faecalis) and Candida albicans (C. albicans), which are the most common resistant pathogenic microorganisms in the root canal. The antibacterial activity of the pastes was measured using a disk diffusion assay. Results: The GC and GC-MS analyses revealed that O. dubium and M. spicata had major compositions of carvacrol (75.8%) and carvone (71.3%), respectively. Antimicrobial activity was found to be significantly higher when study groups with O. dubium essential oil were applied to both E. faecalis and C. albicans. The results also show that M. spicata, together with calcium hydroxide, demonstrated a significant antifungal effect on C. albicans when incubated for 72 h. Conclusions: M. spicata was found to be an effective antimicrobial agent on C. albicans, whereas O. dubium was found to be very effective on both E. faecalis and C. albicans. These data demonstrate that these natural essential oils may be promising candidates for alternative intracanal medicament in future routine clinical applications.