Wetting the dentin is critical to atraumatic restorative treatment. The conventional insertion can be challenging when using high-viscosity glass-ionomer cement. This study evaluated the formation of gaps and voids after three insertion methods using micro-CT. Teeth underwent removal of occlusal and proximal caries through the atraumatic restorative treatment technique. Then, they were fixed in an artificial dental arch to simulate the clinical condition and were restored using three insertion methods: conventional, Centrix injection, and double-filling. Previous dentin conditioning procedures, steel matrix and wooden wedge application, and post-insertion procedures (digital compression and surface protection) were the same. The material was inserted using a manual instrument in the conventional technique and was inserted with a syringe in the Centrix injection group. In the double-filling technique, the tooth received a first layer of a flowable ionomer (through modifying the powder/liquid ratio), and a second layer (with standard ratio) was applied before the final set of the first one. A micro-CT unit scanned each tooth before and after restoration. Each cavity was defined as the volume of interest, and the volumes of gaps and voids were calculated. Data were analyzed using one-way ANOVA and Tukey posthoc test (p < .05). Double-filling had improved filling volume with lower values for gap volume, followed by Centrix injection. The conventional technique had the highest gap volume. No statistically significant difference was observed for void volume. Double-filling demonstrated fewer gaps, followed by Centrix injection, which is critical to obtain better adhesive, remineralizing, and antibacterial activities.