The oxidation of tyrosine residues of silk fibroin involves the generation of dityrosine and 3,4-dihydroxyphenylalanine (DOPA). However, it remains a challenge to selectively control the reaction pathway to produce dityrosine or DOPA in a selective fashion. Here, silk hydrogels with controllable formation of not only dityrosine and DOPA but also DOPA-Fe3+ complexes within the cross-linked networks were developed. The use of chitosan particles in the Fenton reaction allowed the interaction of Fe3+ ions with silk fibroin to be limited through the adsorption of Fe3+ ions onto chitosan particles by manipulating contact time between the reaction medium and chitosan particles. This led to significant suppression of the premature formation of β-sheet structures that cause steric hindrance to the collisions between tyrosyl radicals and thus enabled higher selectivity toward the formation of dityrosine than DOPA. Remarkably, the addition of ethylenediaminetetraacetic acid (EDTA) to the chitosan particle-assisted Fenton reactions resulted in hydrogels that significantly favored the formation of DOPA over dityrosine due to the increase in the hydroxylation of phenol in the presence of EDTA. Despite the existence of Fe3+-EDTA complexes, Raman spectra indicated the DOPA-Fe3+ complexation in the hydrogels. Mechanistically, the hydrogel networks with small-sized and uniformly distributed β-sheet structures as well as the abundance of DOPA appear to make non-EDTA-chelated Fe3+ ions more accessible to complexation with DOPA. These findings have important implications for understanding the oxidation of tyrosine residues of silk fibroin by metal-catalyzed oxidation systems with potential benefits for future studies on silk protein-based hydrogels capable of generating intrinsic adhesive features as well as for exploring dual-cross-linked silk hydrogels constructed by chemical cross-linking and metal-coordinate complexation.