Scaffold fabrication is essential in tissue engineering. Amino acid based poly(ester amide)s (PEAs) have been investigated as scaffold materials due to their non-toxic degradation byproducts, and easily tunable mechanical and biological properties. However, L-aspartic acid functionalized PEAs showed poor morphological stability when immersed in buffer. This work focuses on the further functionalization of L-aspartic acid based PEAs, scaffold fabrication and cross-linking of the scaffold to improve morphological stability. Photo-cross-linkable and thermally cross-linkable PEAs were synthesized successfully and characterized. Two scaffold fabrication methods were applied: 1) electrospinning was applied to photo-cross-linkable PEAs, followed by UV treatment to cross-link electrospun scaffolds; 2) solvent casting/particulate leaching was applied to thermally cross-linkable PEAs with in situ thermal cross-linking. The cross-linking degree was demonstrated with morphological change by immersing the cross-linked scaffold in phosphate-buffered saline. Photo-cross-linking turned out to be insufficient to produce scaffolds that were able to survive in aqueous environment, while in situ thermal cross-linking provided highly-cross-linked scaffold. The existence and use of residual carboxylic groups on scaffolds prepared by both electrospinning was proven by model protein conjugation. Confocal microscopy imaging showed stronger fluorescence on conjugated samples than adsorbed samples