Computed tomography (CT) is a non-invasive imaging technique of interest for the ability to produce cross-sectional images. Micro-CT scanners are widely used in research and industry due to its superior spatial resolution. One recent development in CT technology is use of photon counting detectors (PCDs). These detectors offer advantages such as: improved contrast, spatial resolution, and artifact reduction. This study presents the development of a novel Brazilian micro-CT prototype equipped with PCDs. The micro-CT was developed in modules, capable of supporting and allowing the alignment of the microfocus X-ray tube, sample and detector. The contrast (C) contrast-to-noise ratio (CNR) were the metrics to evaluate the image quality of the images produced by the prototype. The results shows that the CNR increased with the current, indicative of reduced image noise with higher photon counts. However, despite varying imaging parameters, including tube potential and filtration, the contrast remained consistent across all cases, averaging 6.8 ± 0.8%. This result can be indicative of the ability of PCDs to produce images where different energy photons have the same weight. This work lays the foundation for future research aimed at optimizing and validating the performance of PCD-equipped CT systems. Additionally, ongoing efforts will focus on further refining the prototype’s hardware and software.