Background: Caries lesion activity is typically assessed by visual–tactile criteria. Regular monitoring is required to detect the transition of lesions and to ensure that the initial assessment was valid. This clinical study aimed to evaluate the agreement of bioluminescence measurements (Calcivis imaging system, Cis) with visual examination to assess caries lesion activity and to monitor occlusal surfaces. Methods: The occlusal surfaces of ninety-one permanent posterior teeth were assessed for the presence or absence of active caries lesions with ICCMS criteria and Cis measurements at three visit times: baseline (t1) and six months (t2) and 12 months (t3) after baseline. Results: At the baseline visit, 70% of the included occlusal sites were assessed visually as active lesions (ICCMS codes 1 and 2). At t3, 64.8% of the sites showed signs of an active lesion. The percentage agreements between the visual and Cis methods were 87.8% (t1), 89.9% (t2) and 88.6% (t3). The corresponding κ-values were 0.71 (95% CI 0.52;0.87), 0.75 (95% CI 0.59;0.89) and 0.77 (95% CI 0.61;0.90), respectively. No significant difference between the visual and bioluminescence systems was found at any visit (p > 0.05). The results based on cluster randomization (generalized estimation equations) showed no significant differences between the visual and Cis findings for all visits (p = 0.108, Wald Χ2 with 1 df = 2.587). Conclusion: The bioluminescence system demonstrated substantial agreement for the activity assessment of occlusal lesions compared to the findings obtained by visual assessment over twelve months.