The objective of this review is to provide a precise description of the property changes that occur as a result of additive incorporation into polymer filaments. It comprises of the maximum allowable amount of additives that can be incorporated into polymers to enhance properties effectively, and the favorable and unfavorable consequences of additive incorporation in the parts produced by three dimensional printing by material extrusion. This evaluation classifies the incorporation of additives according to their necessary characteristics, including mechanical, electrical, thermal, and biomedical properties. Additionally, the study provides an in-depth analysis of the difficulties encountered throughout the additively fabricated filaments’ fabrication and during the three dimensional printing through material extrusion processes. In addition, the reasons for the deterioration of the material’s properties subsequent to the incorporation of compounds are elucidated. The study incorporated state-of-the-art literature to demonstrate the effects of incorporating additives derived from natural sources, such as discarded coffee grounds, wood flour, and biochar obtained from woody sources, cork powders, and lignin obtained from diverse plant sources. Additives used in polymers have notable impacts on the material’s behaviors, with certain additives enhancing these properties while others degrade the core characteristics. The selection of the additive type and the level of inclusion significantly influence the properties of the polymer composites. Moreover, the extrusion of customized filaments often encounters numerous challenges. However, by employing optimum printing parameters, it is possible to successfully print parts with minimal defects.