Many advanced therapy medicinal products (ATMPs) consist of genetically modified organisms (GMOs). GMOs are defined in European legislation as an organism, with the exception of human beings, in which the genetic material has been altered in a way that does not occur naturally by mating and/or natural recombination. Clinical trial applications (CTAs) and marketing authorisation applications (MAAs) for ATMPs containing GMOs require licenses for use. Unfortunately, the legislation around GMO licenses is variable and interpreted differently in different countries in Europe. Furthermore, there are different requirements in the USA and other countries that add a regulatory and administrative burden to the development of ATMPs. Based on our experience presenting, here we describe some of the key requirements for preparing GMO license requests under different legal bases around the world. The proposals include ideas for analysing the logistical flow of supply, storage, use and disposal of GMOs as well as tips for identification of important data that may be necessary for the completion of the application and for developing an overall global strategy that can save time and resources, thus accelerating clinical availability of ATMPs.