Bioactive compounds (BCs) provide numerous health benefits by interacting with one or more components of living tissues and systems. However, despite their potential health benefits, most of the BCs have low bioaccessibility and bioavailability, hindering their potential health-promoting activities. The conventional encapsulation techniques are time-consuming and have major limitations in their food applications, including the use of non-food grade chemicals, undesired sensory attributes, and storage stability issues. A cutting-edge, new technique based on 3D printing can assist in resolving the problems associated with conventional encapsulation technologies. 3D food printing can help protect BCs by incorporating them precisely into three-dimensional matrices, which can provide (i) protection during storage, (ii) enhanced bioavailability, and (iii) effective delivery and controlled release of BCs. Recently, various 3D printing techniques and inks have been investigated in order to create delivery systems with different compositions and geometries, as well as diverse release patterns. This review emphasizes the advances in 3D printing-based encapsulation approaches, leading to enhanced delivery systems and customized food formulations.