We examine the morphological and chemical changes in the pulp chamber dentin after using endodontic agents by scanning electron microscopy (SEM), Fourier transform Raman spectroscopy (FT-Raman), and micro energy-dispersive x-ray fluorescence spectrometry (). Thirty teeth were sectioned exposing the pulp chamber and divided by six groups (): NT-no treatment; CHX-2% chlorhexidine; CHXE-; E-17% EDTA; SH5-5.25% NaOCl; SH5E-. The inorganic and organic content was analyzed by FT-Raman. examined calcium (Ca) and phosphorus (P) content as well as ratio. Impressions of specimens were evaluated by SEM. Data were submitted to Kruskal-Wallis and Dunn tests (). Differences were observed among groups for the peak. Ca and P content differences were significant (). CHXE and E presented the highest ratio values compared to the other groups (). The SEM images in the EDTA-treated groups had the highest number of open tubules. Erosion in the tubules was observed in CHX and SH5E groups. Endodontic agents change the inorganic and organic content of pulp chamber dentin. NaOCl used alone, or in association with EDTA, was the most effective agent considering chemical and morphological approaches.