Bulk-fill composites enable timesaving and less technical-sensitive application of restorations. This study investigated and compared the marginal integrity of classical and bulk-fill composite restorations in primary and permanent molars before and after thermo-mechanical loading (TML). Two Class II cavities were prepared in each of 20 primary and 20 permanent molars. The molars were randomised in four groups for each molar type. Groups 1 and 5 were restored with a high-viscous bulk-fill composite (Tetric PowerFill), groups 2 and 6 were restored with a flowable bulk-fill composite (Tetric PowerFlow), groups 3 and 7 were restored with a high-viscous classical composite (Tetric Prime), and groups 4 and 8 were restored with a flowable classical composite (Tetric EvoFlow). In permanent molars, the flowable composites were covered with a 2-mm layer of high-viscous composite (groups 6 and 8). The restorations were subjected to TML in a custom-made chewing machine (5–50 °C, 2 min dwelling time, × 1000; 400 ,000 loading cycles, 1.7 Hz, 49 N), and quantitative marginal analysis was conducted using scanning electron microscopy. Marginal integrity of each restoration was calculated as a percentage of continuous margins before and after TML. The tested high-viscous bulk-fill restoration showed similarly high marginal integrity in primary and permanent molars as the classical restoration. The tested flowable bulk-fill restoration showed the lowest marginal integrity compared to all other restorations after TML. In contrast to flowable bulk-fill restorations, high-viscous bulk-fill restorations show similar marginal integrity as classical hybrid composite restorations after TML, in both primary and permanent molars.