A packaging system and associated method for use with a pharmaceutical dispenser provides a turnkey solution for packaging pharmaceutical products such as solid medications and nutritional supplements to be taken orally in health care settings, including but not limited to long term care (LTC) and assisted living settings. An overall pharmacy system and methodology begins with bulk medications and supplements introduced into the work flow, individually packaged and assembled into medpass orders per patient and delivered to the LTC facility or other institution for patient consumption. The process begins by converting bulk medications and supplements to packaged unit doses and ultimately individually packaged medpass bags for each patient on a 24-hour schedule. The design of the overall system and its individual components allows for physical control of each unit dose package from start to finish without any unit dose package “free fall” in the system.