For bridge deck applications, laser-welded corrugated core steel sandwich panels with dual weld lines per crest and trough have been shown to be highly material- and economically efficient. The nature of welding induces a variation in the geometric properties of the joint that connects the core to the faces. The geometric properties of the joint are the weld width, weld misalignment, and plate gap between the core and the faces. This paper aims to investigate the impact of the variation of the production-dependent geometric properties of the joint on the fatigue-relevant stresses. A secondary aim of this paper is to investigate the impact of contact between the core and the faces on the weld region stresses. Within this paper, the production of four sandwich panels is documented and the manufacturing-dependent geometric properties of their joints are quantified. In order to investigate the impact of the natural variation of the parameters, a parametric study based on finite element analyses is executed. The result of the parametric study shows, among several other findings, that misalignment of the weld line in relation to the core direction can lead to considerable increases in stresses, determinant for the fatigue life of the panel.