Flux-cored wires are commonly used in structural and pipeline welding, shipbuilding, offshore constructions, and petrochemical and power generation industries. The higher heat inputs in the multi-pass welding result in shorter production time while considerably changing the properties of the welded joint. In this study, robotic flux cored arc welding with varying heat inputs (between 0.56-2.52 kJ/mm) was performed to determine the effect of heat input on weld microstructure, hardness, tensile properties, and impact toughness in the structural steel joints. Results exhibited that decrease in heat input from 2.52 to 0.56 kJ/mm changed the majority of the microstructure from polygonal ferrite to acicular ferrite. Furthermore, this increased by 56%, 37%, and 47% in yield strength, tensile strength, and hardness values, respectively, while decreasing by 30% and 15% in elongation and Charpy impact test results, respectively. Moreover, all welded joints displayed a satisfying toughness value higher than the requested value of 47 J, even at the test temperature of -50 °C. Finally, it can be concluded that the optimum results were obtained with a heat input of 1.26 kJ/mm, considering the minimum requirements of the AWS A5.20 standard and the expectations in applications.