In this study, the influence of physio-chemical properties of four printing substrates, fibrous papers (filter, bulky, recycled), and polymer film (synthetic paper) on the size of the thermochromic (TC) prints microcapsules was investigated. Results indicate that interaction between thermochromic ink and printing substrate determine the print morphology, i.e., porosity and roughness of printing substrate affect dimensions of TC microcapsules of resulting prints, while ink adhesion affects dimensional changes during heating–cooling cycle. Atomic force microscopy (AFM) analysis showed that microcapsules of the prints, on the surface of the smoothest synthetic paper, possess the smallest diameter and height, while, on the most porous and the most roughened surface of F paper, the microcapsules of the prints possess the highest diameter and height. By increasing the temperature to 40 °C, the biggest changes in the shape of the microcapsules (increase in height and decrease in diameter) were obtained using the surface of the hydrophilic filter paper. While using the recycled paper surface, the situation is opposite; the height and diameter of the microcapsules are reduced, and the microcapsules penetrate deeper into the paper structure (due to optimum adhesion). On the bulky paper surfaces, which are more hydrophobic than recycled paper (higher interfacial tension), the increase of temperature does not cause any significant changes in the shape and position of the microcapsules. The same behavior is observed using hydrophobic non-porous synthetic paper.