The manufacturing process for in vitro tissue culture products and medical devices relies on a validated sterilization route for ensuring product sterility, safety and performance. Two key aspects that contribute toward final sterilization validation are (1) the reliable estimation of product bioburden and (2) the development of a proficient sterile packaging system. Bioabsorbable composite systems and architecture of tissue scaffolds can lead to numerous challenges for bioburden testing and packaging design. This study is concerned with the development of bioburden assessment methods and packaging systems for Variotis™; a soft tissue engineering scaffold. A bioburden test method relying on mechanical agitation was established. Bioburden assessment was achieved by recovering Geobacillus stearothermophilus spore inoculant for analysis. A packaging system was developed which provides adequate protection for Variotis™ scaffolds while meeting other user/sterilization requirements for research grade product. The guidelines and design approaches included in this study are generally applicable to other tissue engineering scaffold and medical devices.