The field of tissue engineering is constantly evolving as it aims to develop bioengineered and functional tissues and organs for repair or replacement. Due to their large surface area and ability to interact with proteins and peptides, graphene oxides offer valuable physiochemical and biological features for biomedical applications and have been successfully employed for optimizing scaffold architectures for a wide range of organs, from the skin to cardiac tissue. This review critically focuses on opportunities to employ protein–graphene oxide structures either as nanocomposites or as biocomplexes and highlights the effects of carbonaceous nanostructures on protein conformation and structural stability for applications in tissue engineering and regenerative medicine. Herein, recent applications and the biological activity of nanocomposite bioconjugates are analyzed with respect to cell viability and proliferation, along with the ability of these constructs to sustain the formation of new and functional tissue. Novel strategies and approaches based on stem cell therapy, as well as the involvement of the extracellular matrix in the design of smart nanoplatforms, are discussed.