Wire Arc Additive Manufacturing (WAAM) of thin walls is an adequate technology for producing functional components made with aluminium alloys. The AlMg5 family is one of the most applicable alloys for WAAM. However, WAAM differs from traditional fabrication routes by imposing multiple thermal cycles on the material, leading the alloy to undergo cyclic thermal treatments. Depending on the heat source used, thermal fluctuation can also impact the microstructure of the builds and, consequently, the mechanical properties. No known publications discuss the effects of these two WAAM characteristics on the built microstructure. To study the influence of multiple thermal cycles and heat source-related thermal fluctuations, a thin wall was built using CMT-WAAM on a laboratory scale. Cross-sections of the wall were metallographically analysed, at the centre of a layer that was re-treated, and a region at the transition between two layers. The focus was the solidification modes and solubilisation and precipitations of secondary phases. Samples from the wall were post-heat treated in-furnace with different soaking temperatures and cooling, to support the results. Using numerical simulations, the progressive thermal cycles acting on the HAZ of one layer were simplified by a temperature sequence with a range of peak temperatures. The results showed that different zones are formed along the layers, either as a result of the imposed thermal cycling or the solidification mode resulting from CMT-WAAM deposition. In the zones, a band composed of coarse dendrites and an interdendritic phase and another band formed by alternating sizes of cells coexisted with the fusion and heat-affected zones. The numerical simulation revealed that the thermal cycling did not significantly promote the precipitation of second-phase particles.