The classificatory method is considered a straightforward and robust procedure for the assessment of welded joints in metallic structures. The methodology adopts a set of S–N diagrams with a conservative survival rate, which expresses the fatigue performance of the most employed joint configurations. In the design phase, the adoption of a structural detail correlated with a higher curve in the set conducts to high structural integrity. Nevertheless, fatigue phenomenon is essentially multifactorial and, consequently, several optimizing alternatives may be applied for life increasing. Studies focused on continuous (weldless) parts correlate fatigue performance with the material ultimate strength. Transferring this approach to welded parts, adoption of a high-strength filler metal, or any procedure intended to mitigate metallurgical inhomogeneity in the weld-affected region may propitiate fatigue life improvement. In other sense, issues related to bead geometry, notably the notch effect associated with weld toe, are also reported to have an essential influence on fatigue life of structural details. This work aims to counterbalance material and bead geometry aspects related to fatigue performance of butt joints subjected to repeated transverse loading. Two welding processes, FCAW and GMAW, as well as different filler metals and parameters, were adopted for specimens manufacturing. The ASTM-A572-Gr.50 steel was employed as a parent metal. After welding, FCAW joints presented better mechanical and metallurgical characteristics. Additionally, in order to characterize the relevance of the notch effect, half of the specimens had the original bead geometry maintained, while the others underwent a manual removal of the reinforcement. The obtained results indicate that FCAW joints present better fatigue performance in the as-welded state. However, after removing the reinforcements, both welding processes attained similar results, suggesting that the notch effect has more relevance for fatigue life than mechanical and metallurgical characteristics of the joint. Consequently, the superior performance presented by the FCAW joints in the as-welded state is assigned to the final shape of the reinforcements, which is smoother than in the GMAW case. The higher capacity of penetration and better filler metal wettability propitiated by the FCAW process is responsible for the lower notch effect.