This study investigated the effects of biofilm removal from the tooth-restoration surface on secondary caries lesion progression. Biofilms were grown for up to 28 days on resin-restored enamel-dentin disks with an interfacial gap with DMM or DMM + 1% sucrose under five different protocols of Visible Biofilm Removal (V-BR; n = 7): (1) without V-BR, (2) with partial V-BR, (3) with total V-BR, (4) with total V-BR and saliva reinoculation, and (5) without V-BR under 9 h of cariogenic challenge. V-BR was performed at 7, 14 and 21 days. ΔS and CFU counts served as outcome variables. Linear regression models showed that ΔS values were higher for outer lesions than wall lesions, and outer lesion progression generally increased over time (p < 0.01). All protocols tested, except total V-BR, increased the lactobacilli count (p < 0.005). V-BR did not influence the progression of caries lesions on the cavity wall in this biofilm model.