Objectives. The objective of this study was to determine the effects of antimicrobial photo dynamic therapy (aPDT) with indocyanine green (ICG) and toluidine blue (TB) on protease activity (matrix-bound cathepsin K and matrix metalloproteinase (MMP) and dentin bond strength. Methods. Caries-free human third molars were assigned to five groups: 1-control group, 2-application of ICG with activation using an 810 nm diode (aPDT), 3-application of ICG, 4-application of TB with activation using a 660 nm diode (aPDT), and 5-application of TB. For the enzymatic investigation, dentin beams were incubated for either 3 days or 3 weeks. Aliquots of the incubation media were analyzed by ELISA for CTX (C-terminal cross linked telopeptide of type I Collagen) and ICTP (cross-linked carboxy-terminal telopeptide of type I collagen). For microtensile bond strength testing (mu TBS), composite resins were layered onto the tooth surface; the samples were then subjected to mu TBS. Kruskall-Wallis and Mann-Whitney U tests were applied for statistical analysis of CTX and ICTP, one wayANOVA and Tukey's test were applied for statistical analysis of mu TBS. Results. Pretreating the dentin matrices with aPDT decreased the endogenous protease activity. ICG with laser activation resulted in the highest mu TBS. Therefore, aPDT should be considered as a treatment method because it can reduce MMP-mediated dentin degradation and increase the mu TBS. Significance. Inhibiting endogenous protease activity improves the stability of the dentin-adhesive bond and the durability of the bond strength. (c) 2021 The Academy of Dental Materials. Published by Elsevier Inc. All rights reserved.