Introduction: The absence of a barrier in an open root apex makes endodontic treatment challenging as root-filling material can easily reach the surrounding tissue. The aim of the study was to compare the apical microleakage associated with mineral trioxide aggregate (MTA), biodentine, custom-made gutta-percha with MTA plus and custom-made gutta-percha with Adseal in immature permanent teeth by dye penetration method. Methods: Apical 2 mm of 60 single-rooted mandibular premolar teeth was resected to create divergent open apices and 10 teeth each were filled with Biodentine plug, MTA plug, custom-made gutta-percha with MTA plus sealer and custom-made gutta-percha with Adseal sealer. Ten teeth each acted as positive and negative controls. All the samples were stored at 37°C at 100% humidity for 5 weeks and then immersed in 2% Rhodamine B dye for 24 h. Transverse sectioning was done apically at 1 mm and 3 mm to evaluate dye penetration under a fluorescence microscope using ImageJ software. Results: There was a significantly greater microleakage at 1 mm cross section compared to 3 mm (p < 0.0001). At 1 mm cross section, the apical microleakage was the highest for the MTA plug with a mean leakage percentage of 48.08 ± 16.38, a mean depth of leakage of 0.46 ± 0.10 mm and a mean area of leakage of 1.35 ± 0.74 mm2, compared to other groups, and the difference was statistically significant. However, at a 3 mm cross section, MTA plus sealer with gutta-percha demonstrated the highest mean leakage percentage (25.01 ± 7.77) compared to other groups and the difference was statistically significant (p = 0.03). Conclusion: It can be concluded that the 3-mm-thick apical plug provided better sealing of the open apex compared to the 1 mm apical plug and there was no significant difference in microleakage among the Biodentine plug, MTA plug and Adseal sealer with gutta-percha plug at 3 mm cross section.