The strategy of combining biomolecules and synthetic components to develop biohybrids is becoming increasingly popular for preparing highly customized and biocompatible functional materials. Carbon nanotubes (CNTs) benefit from bioconjugation, allowing their excellent properties to be applied to biomedical applications. This study reviews the state-of-the-art research in biomolecule–CNT conjugates and discusses strategies for their self-assembly into hierarchical structures. The review focuses on various highly ordered structures and the interesting properties resulting from the structural order. Hence, CNTs conjugated with the most relevant biomolecules, such as nucleic acids, peptides, proteins, saccharides, and lipids are discussed. The resulting well-defined composites allow the nanoscale properties of the CNTs to be exploited at the micro- and macroscale, with potential applications in tissue engineering, sensors, and wearable electronics. This review presents the underlying chemistry behind the CNT-based biohybrid materials and discusses the future directions of the field.