The aim of this work is to assess the crystalline structure modification of an SLM Co-Cr-W dental alloy, veneered with two different ceramics, by means of X-ray diffraction (XRD), atomic force microscopy (AFM), and scanning electron microscopy, coupled with energy-dispersive spectroscopy (SEM-EDS). Ten identical plates were fabricated using SLM and were subsequently subjected to ceramic veneering. Following the repeated firing of the ceramic layers, carried out at temperatures exceeding 900 °C, new crystalline phases and variations in the crystallite sizes in the SLM Co-Cr-W dental alloy used for the substructure were detected via XRD. The two veneering ceramics showed significant differences in their behavior, beginning with the first firing, accompanied by structural changes. AFM micrographs and histograms of the surface heights over the whole scanned area of the samples showed that the surface of the Co-Cr-W dental alloy is strongly affected by the repeated firings necessitated by the ceramic firing process, a finding in accordance with the XRD results. The SEM investigation revealed that the different firing parameters had an impact on the alloy, the ceramic microstructure, and the surface quality. The differences in the chemical composition of the ceramics, highlighted by EDS, are reflected in their behavior. The crystalline alloy structure is influenced by the repeated firings of the ceramic layers.