Objective: To assess the agreement in detecting and monitoring occlusal caries over thirty months using conventional visual and radiographic assessment and an intraoral scanner system which supports automated caries scoring. Methods: Ninety-one young participants aged 12–19 years were included in the study. All occlusal surfaces were examined visually, radiographically (when indicated), and scanned with the TRIOS 4 intraoral scanner. TRIOS Patient Monitoring software (vers. 2.3, 3Shape TRIOS A/S, Denmark) was used for automated caries detection on the 3D digital models. Results: Fifty-five of the study participants were re-examined after 30-months. Significant differences regarding caries detection were found between the conventional methods and the automated caries scoring system (p < 0.01), with moderate positive percent agreement (49–61%) and high negative percent agreement (87–98%). All methods reported significant caries progression over the follow-up period (p < 0.01). However, the automated system showed significantly more caries progression than the other methods (p < 0.01). Conclusions: The software for automated caries detection and classification showed moderate positive agreement and strong negative agreement with the conventional methods considering both the baseline and the follow-up assessments. The automated caries scoring system detected significantly fewer caries lesions and tended to underestimate the caries severity. All methods indicated significant caries progression over the follow-up period, while the automated system detected more caries progression. Clinical significance: The TRIOS system supporting automated occlusal caries detection and classification can assist in detecting and monitoring occlusal caries on permanent teeth as a complementary tool to the conventional methods. However, the operator should be aware that the automated system shows a tendency to underestimate the caries presence and lesion severity.