Advanced therapy medicinal products (ATMPs) are becoming the new kid on the block for the treatment of a variety of indications with promising results. Academic centres have often been at the forefront of basic research, preclinical phases, and translational studies for the clinical development of ATMPs for several approved drugs. Despite the academic contribution to the basic and clinical research of ATMPs, undertaking a full product development process is extraordinarily challenging and demanding for academic institutions. Meeting regulatory requirements is probably the most challenging aspect for academic development, considering the limited experience and resources compared with pharmaceutical companies. The aim of this review is to present and discuss the key aspects to be considered when developing novel ATMPs from an academic perspective, based on our own experience. Emphasis is placed on understanding the regulatory requirements during the early phases of the drug development process, particularly for the preparation of a Clinical Trial Application. In general, academic centres do not possess experience in product-related documentation (such as the Investigational Medicinal Product Dossier), and therefore, early interaction with regulators is crucial to understand their requirements and receive guidance to comply with them. Tips are provided on how to manage quality, non-clinical, clinical, and risk and benefit documentation, based on our own experience and challenges. We believe this review will contribute to providing key regulatory knowledge to academic and clinical environments with the purpose of smoothing the regulatory path of ATMPs.