Restoring first permanent molars affected with molar incisor hypomineralization (MIH) is challenging. Focusing on improving the quality of life for children affected by MIH, at least until the complete eruption of first permanent molars to receive full coverage, to decrease the hypersensitivity and to be able to perform proper oral hygiene measures, the purpose of this study was to compare silver modified atraumatic restorative technique (SMART) versus the conventional restoration and fluoride varnish application on moderate to severe hypomineralized molars. The comparison considered the restoration survival, hypersensitivity, and digital surface area changes after one year follow up. Twenty-eight children were selected (20 girls and 8 boys) with at least 2 MIH molars with the same defect severity. The study comprised 2 groups; MOD group (moderate hypomineralized molar severity) and SEV group (Severe hypomineralized molar severity) (n = 28 tooth). Each group was further subdivided into 2 subgroups according to the technique of restoration: SMART subgroup and CONV subgroup (high viscosity glass ionomer restoration and fluoride varnish application) (each = 14 tooth). Evaluation was done in terms of the restoration survival (6 months and 12 months), hypersensitivity at 1 weak, 6 months and 12 months and occlusal surface area changes at 12 months). Professional Fluoride varnish application and home prophylaxis using MI paste were the protocol for each child patient. There was no significant difference between the 4 subgroups, regarding tooth restoration integrity at 6-months vs. 12-months. However, a statistically significant difference in tooth restoration integrity between the 4 subgroups at 12-months (P = .049). Also, the hypersensitivity score, there was a statistically significant difference between the 4-time intervals (P < .001) and a statistically significant difference in surface area changes between the 4 subgroups. Selective removal of carious tissue and SMART restoration, combined with dental home and professional preventive measures every 3 months maintained the integrity of restorations in severely and moderately affected permanent molars up to 1 year. The study protocol was retrospectively registered on Clinical Trials (NCT05931822-05/ 07/2023).