With advantageous biomechanical properties, materials derived from ex vivo tissues are being actively investigated as scaffolds for tissue engineering applications. However, decellularization treatments are required before implantation to reduce the materials immune impact. The aim of these investigations was to assess a convective flow model as an enhanced methodology to decellularize ex vivo tissue. Isolated human umbilical veins were decellularized using two methods: rotary agitation at 100 rpm on orbital shaker plates, and convective flow run at 5, 50, and 150 mmHg within perfusion bioreactors. Extracted phospholipids and total soluble protein were assessed over time. Histology, SEM, and uniaxial tensile testing analysis were carried out to evaluate variation in the tissues. After 72 h, samples exposed to traditional rotary agitation showed retention of whole cells and cellular components, whereas pressure-based systems showed no visual sign of cells. The convective flow method was significantly more effective at removing phospholipid and total protein than the agitation model. High transmembrane pressure (150 mmHg) resulted in higher phospholipids extraction. However, a more efficient protein extraction occurred at 50 mmHg. Variation in extraction rates was dependent on tissue permeability, which varied as pressure increased. Collectively, these findings show significant improvements in decellularization efficiency that may lead to more immune compliant ex vivo-derived biomaterials.