The aim of this study was to assess the performance of the fluorescence camera device VistaCam iX (VC) for the control of caries excavation compared to visual assessment and bacteriological evaluation. Twenty-three patients with 32 dentinal carious lesions were included in the study. The lesions were classified using the International Caries Detection and Assessment System. Fluorescence images were taken at the surface of each lesion using the VC before excavation (stage 1), during (stage 2) and after excavation (stage 3). At each stage, dentine samples were collected. All cavities were closed after excavation using permanent fillings. Bacteria were counted within each dentine sample using flow cytometry. Significant moderate correlation between the fluorescence readings and the bacteria count was found at stage 3 (Spearman correlation coefficient rs = 0.40, p = 0.027). Area under the ROC curve (AUC) was calculated for fluorescence readings and bacteria count using the clinical status at stage 3 as a reference. AUC was 0.954 for the VC readings and 0.797 for bacteria count. Using the median bacteria count at stage 3 as a reference, the AUC for the fluorescence readings was 0.753. The results indicate that the fluorescence camera appears to be a useful supplementary tool in assessing the endpoint of caries excavation with the advantage of enabling data to be digitally visualized and stored. When an experienced dental clinician determined the excavation endpoint, the performance with respect to remaining bacteria count was good.