Nowadays, on-machine tool measurement (OMM) and coordinate measuring machine measurement (CMM) are the most common inspection methods. Although the ex-situ CMM measurements usually offers higher accuracy and reliability, OMM can inspect the workpiece without removing it from the machine tool. Therefore, it is possible to perform both in-process and post-process measurements, avoiding possible unclamping errors. However, due to the non-constant conditions in which machine tools usually operate, it is difficult to guarantee the traceability of measurements over time. For example, thermal fluctuations become a potential source of uncertainty.This paper presents a methodology for ensuring the traceability of OMM on shop floor conditions. For this purpose, several features of a prismatic workpiece are measured on a five-axis machining center. The measurement results and its corresponding uncertainty budget are presented. For the uncertainty estimation the substitution method based on ISO 15530-3:2011 standard is used. In order to identify the impact of the different error sources on the results, a breakdown of the relative weights of the factors that may have an influence on the uncertainties is also given,