Poly(ε-caprolactone) (PCL)-incorporated lignin-chitosan biomass-based nanocomposite porous scaffolds have been effectively prepared by templating oil-in-water Pickering high internal phase emulsions (HIPEs). PCL is dissolved in oil and chitosan and lignin nanoparticles originate in water. The continuous phase of the emulsions is gelled by cross-linking of chitosan with genipin and then freeze-dried to obtain porous scaffolds. The resulting scaffolds display interconnected and tunable pore structures. An increase in PCL content increases the mechanical strength and greatly reduces the water absorption capacity of the scaffolds. Scaffolds loaded with the anti-bacterial drug enrofloxacin show a slow drug release profile, adjustable release rate, and favorable long-term anti-bacterial activity. Moreover, Pickering emulsion templates with suitable viscosity are used as 3D printing inks to construct porous scaffolds with personalized geometry. The results imply that the simplicity and versatility of the technique of combining freeze-drying with Pickering HIPE templates is a promising approach to fabricate hydrophobic biopolymer-incorporated biomass-based nanocomposite porous scaffolds for biomedical applications.