Micro-injection molding (µIM) is a widespread process for the production of plastic parts with at least one dimension, or feature, in the microscale (conventionally below 500 µm). Despite injection molding being recognized as a robust process for obtaining parts with high geometry accuracy, one last occurrence remains a challenge in micro-injection molding, especially when junctions are present on the parts: the so-called weld lines. As weld lines are crucial in determining mechanical part performances, it is mandatory to clarify weld line position and characteristics, especially at the industrial scale during mold design, to limit failure causes. Many works deal with weld lines and their dependence on processing parameters for conventional injection molding, but only a few works focus on the weld line in µIM. This work examines the influence of mold temperature on the weld line position and strength by both experimental and simulation approaches in µIM. At mold temperatures below 100 °C, only short shots were obtained in the chosen cavity. At increased mold temperatures, weld lines show up to a 40% decrease in the whole length, and the overall tensile modulus doubles. This finding can be attributed to the reduction of the orientation at the weld line location favored by high mold temperatures. Moldflow simulations consistently reproduce the main features of the process, weld line position and length. The discrepancy between experimental and simulated results was attributed to the fact that crystallization in flow conditions was not accounted for in the model.