Background An occurrence of secondary caries around the indirect restoration margin is reported to remain a leading cause of failures. Objective This study aimed to test the interfacial microleakage of conventional glass-ionomer (CGI), resin-modified glass ionomer (RMGI) and Nano-hybrid composite (CR) restorations at a full veneer margin crown. Methods Ninety human extracted molar teeth were divided into three groups (n = 30). Each group was subdivided into three subgroups (n = 10) according to the extent of the structural defects; The structural defect in G1 had a depth of 1.5 mm, width and length at 2 mm and 1 mm intrusion within the crown cervical margin. The corresponding structural defect dimension values for G2 were 2, 5, 4 and 2 mm with defects extending onto the root structure. Meanwhile, G3: structural deficiency of 2 mm depth, 3 mm width and 3 mm length and with 1.5 mm extension into the prepared teeth. These structural defects in each subgroup were restored with CGI, RMGI and CR. Artificial carious lesion formation was induced at the cervical finish line with a demineralizing solution. The artificial carious lesions were restored as per the group distribution. Subsequently, teeth samples were prepared and cemented with Nickel-chromium full coverage restorations utilizing glass-ionomer luting cement. Teeth samples were thermocycled, isolated with nail varnish, and immersed in 0.1% methylene blue for 24 h. The teeth samples were sectioned longitudinally, dye penetration was evaluated with a stereomicroscope. The data were analyzed with Kruskal–Wallis and Mann–Whitney U tests. Results CGI-G1 recorded the highest micro-leakage score at 1.450; while CR-G3 recorded the least score (0.350). At a cementum-restoration interface, CR-G1 (0.850) documented the lowest micro-leakage; RMGI-G3 had a greater value at 1.700. Conclusions The hybrid CR could be effectively used to restore the restoration of a marginal gap around crown margins.