An intermetallic layer (IML) between the solder alloy and the soldered surface affects the mechanical and electrical performance of the resulting joints. Numerous studies have explored the possibilities of influencing the IML to achieve more reliable interconnections. However, the type and composition of the used flux, crucial for the proper creation of solder joints, is rarely included as a possible influencing factor. In this article, a comprehensive study on the interfacial microstructure evolution of lead‐free SnAgCu solder joints, accounting for the flux type and the temperature of the preheating phase of reflow soldering, where the flux contained in the solder paste becomes active, is presented. In the results, it is shown that the IML of as‐reflowed and thermally aged solder joints depends significantly on the flux. The IML activation energy is 57% higher for rosin‐based low‐activity (ROL)0 flux compared to ROL1 flux. The ROL0 flux, containing fewer active components, also outperforms the ROL1 flux in both the mechanical and electrical properties of the joints. Furthermore, the temperature profiles also show slight differences in measured properties, with the fluxes responding differently to changes in preheating temperature. In the presented results, importance of the used flux on solder joint microstructure is demonstrated.