Shape memory polymers (SMP) are used in the three-dimensional (3D) printing field for different applications such as soft robotics or medical devices. Although this technology has expanded the capabilities of additive manufacturing, there still exists fundamental questions regarding the optimum condition for manufacturing these 3D-printed parts. Various factors play a crucial role in the final quality of printed parts, such as deposition orientation, percentage infill, or environmental conditions. In this paper, we study the effect of humidity on commercially available shape memory polymers (SMPs) (NinjaFlex©) at both micro- and macroscale. By performing a 3D computational fluid dynamic model for the printing environment, it is found there are significant temperature and humidity fluctuations around the hot-end and printing bed. Macroscale characterization through ASTM D638 tensile testing shows that for humidity levels higher than 60%, there is a 5–10% reduction in the strength of the material (ultimate strength and tangent modulus). This study is verified by microscale characterization performed with atomic force microscopy on thin films. It is shown that in addition to the effect of humidity on the stiffness of materials, there is an effect on the loss moduli of the matter as well. As humidity increases, these polymers become more viscoelastic. Simultaneously, it is shown higher humidity levels cause increased micro-level surface roughness, which can be the cause for the strength reduction for higher humidities.