An automated programmable processor-controlled system and related methods for packaging an agricultural sample such as soil for testing for various chemical properties such as plant available nutrients. The packaging system includes a sample packaging apparatus processes raw bulk sample material collected in the agricultural field to be expediently and conveniently containerized for processing and analysis. The apparatus may include a grinder, compactor, container magazine, and rotatable carousel which carries a sample container between various processing stations. Bulk sample material is reduced in particle size by the grinder which is then transferred to the compactor. An actuated plunger fills and compacts the sample material into the sample container. A decapper automatically both removes and replaces the container cap before and after filling respectfully. An RFID device reads the container ID tag and writes the GPS sample collection location to the tag. The system is controlled by one or more programmable processors.