A system for generating a supplement instruction set using artificial intelligence. The system includes at least a server wherein the at least a server is designed and configured to receive training data. The system includes a diagnostic engine operating on the at least a server designed and configured to record at least a biological extraction from a user and generate a diagnostic output based on the at least a biological extraction and training data. The system includes a plan generator module operating on the at least a server designed and configured to generate a comprehensive instruction set associated with the user as a function of the diagnostic output. The system includes a supplement plan generator module operating on the at least a server designed and configured to generate a supplement instruction set as a function of the comprehensive instruction set.