Academic institutions coin the ATMP landscape but do not possess an industry-like capacity to vigorously pursue the full developmental pathway to marketing authorization. At the same time, industry has fostered clinical trials with ATMPs, brought the first products to marketing authorization, and defined novel modes of interaction with academia. A regulatory niche for local manufacturing of ATMPs within an academic institution had been foreseen in Regulation (EU) 1394/2007 under the term “Hospital Exemption” but remained ill-defined. Manufacture in close proximity to the patient is difficult to accomplish, as “point of care” systems for the manufacture of ATMPs have encountered regulatory challenges hovering between process and product. The efforts and costs for the development of ATMPs continue to be dramatically underestimated, and few academic centers were persistent enough to invest in the GMP infrastructure needed and to recruit personnel trained in ATMP development. As a consequence, the contribution by hospitals to ATMP development has shifted from the finished ATMP toward the procurement of starting materials, selected manufacturing steps, storage of the product, clinical application, and participation in clinical trials. As the development and use of cell-based therapies and ATMPs continue to attract and challenge clinicians and scientists, this review aims to discuss logistical, financial, and regulatory issues that might contribute to the changing role of Academia in ATMP development, with an outlook into possible developments in the future and proposals for ways to reshape the academic environment under the auspices of what might truly have been meant by the hospital exemption clause.