Fabricating three-dimensional (3D) porous scaffolds with controlled structure and geometry is crucial for tissue regeneration. To date, exploration in printing 3D natural protein scaffolds is limited. In this study, soy protein slurry was successfully printed using the 3D Bioplotter to form scaffolds. A method to verify the structural integrity of resulting scaffolds during printing was developed. This process involved measuring the mass extrusion flow rate of the slurry from the instrument, which was directly affected by the extrusion pressure and the soy protein slurry properties. The optimal mass flow rate for printing soy slurry at 27°C was 0.0072±0.0002 g/s. The addition of dithiothreitol to soy slurries demonstrated the importance of disulfide bonds in forming solid structures upon printing. Resulting Bioplotted soy protein scaffolds were cured using 95% ethanol and post-treated using dehydrothermal treatment (DHT), a combination of freeze-drying and DHT, and chemical crosslinking using 1-ethyl-3-(3 dimethylaminopropyl)carbodiimide (EDC) chemistry. Surface morphologies of the different treatment groups were characterized using scanning electron microscopy. Scaffold properties, including relative crosslink density, mass loss upon rinsing, and compressive modulus revealed that EDC crosslinked scaffolds were the most robust with moduli of approximately 4 kPa. Scaffold geometry (45° and 90° layer rotations) affected the mechanical properties for DHT and EDC crosslinked scaffolds. Seeding efficiency of human mesenchymal stem cells (hMSC) was highest for nontreated and thermally treated scaffolds, and all scaffolds supported hMSC viability over time.