Additive production is currently perceived as an advanced technology, where intensive research is carried out in two basic directions—modifications of existing printing materials and the evaluation of mechanical properties depending on individual production parameters and the technology used. The current research is focused on the evaluation of the fatigue behavior of 3D-printed test specimens made of pure PLA and PLA reinforced with filler based on pinewood, bamboo, and cork using FDM (fused deposition modeling) technology. This research was carried out in response to the growing demand for filaments from biodegradable materials. This article describes the results of tensile fatigue tests and image analysis of the fracture surface determined by the SEM method. Biodegradable PLA-based materials have their limitations that influence their applicability in practice. One of these limitations is fatigue life, which is the cyclic load interval exceeding 50% of the tensile strength determined in a static test. Comparison of the cyclic fatigue test results for pure PLA and PLA reinforced with natural reinforcement, e.g., pinewood, bamboo, and cork, showed that, under the same loading conditions, the fatigue life of the 3D-printed specimens was similar, i.e., the filler did not reduce the material’s ability to respond to low-cycle fatigue. Cyclic testing did not have a significant effect on the change in tensile strength and associated durability during this loading interval for PLA-based materials reinforced with biological filler. Under cyclic loading, the visco-elastic behavior of the tested materials was found to increase with increasing values of cyclic loading of 30%, 50% and 70%, and the permanent deformation of the tested materials, i.e., viscoelastic behavior (creep), also increased. SEM analysis showed the presence of porosity, interlayer disturbances, and at the same time good interfacial compatibility of PLA with the biological filler.