Multifunctional nanocarriers enhance the treatment efficacy for modern therapeutics and have gained increasing importance in biomedical research. Codelivery of multiple bioactive molecules enables synergistic therapies. Coencapsulation of cargo molecules into one nanocarrier system is challenging due to different physicochemical properties of the cargo molecules. Additionally, coencapsulation of multiple molecules simultaneously shall proceed with high control and efficiency. Orthogonal approaches for the preparation of nanocarriers are essential to encapsulate sensitive bioactive molecules while preserving their bioactivity. Preparation of nanocarriers by physical processes (i.e., self‐assembly or coacervation) and chemical reactions (i.e., click reactions, polymerizations, etc.) are considered as orthogonal methods to most cargo molecules. This review shall act as a guideline to allow the reader to select a suitable preparation protocol for a desired nanocarrier system. This article helps to select for combinations of cargo molecules (hydrophilic‐hydrophobic, small‐macro, organic–inorganic) with nanocarrier material and synthesis protocols. The focus of this article lies on the coencapsulation of multiple cargo molecules into biocompatible and biodegradable nanocarriers prepared by orthogonal strategies. With this toolbox, the selection of a preparation method for a known set of cargo molecules to prepare the desired biodegradable and loaded nanocarrier shall be provided.