Here we show that the efficacy of the chitosan interaction with diglycidyl ethers of glycols significantly depends on pH and the nature of acid used to dissolve chitosan. In solutions of hydrochloric acid, cross-linking with diglycidyl ethers of ethylene glycol (EGDGE) and polyethylene glycol (PEGDGE) at room and subzero temperatures yields mechanically stable chitosan gels and cryogels, while in acetic acid solutions only weak chitosan gels can be formed under the same conditions. A combination of elemental analysis, FT-IR spectroscopy, and solid state 13C and 15N NMR spectroscopy was used to elucidate possible differences in the mechanism of chitosan cross-linking in alkaline and acidic media at room and subzero temperatures. We have proved that in acidic media diglycidyl ethers of glycols interacted with chitosan mainly via hydroxyl groups at the C6 position of the glucosamine unit. Besides, not only cross-linkages but also grafts were formed at room temperature. The cryo-concentration effect facilitates cross-linkages formation at -10 °C and, despite lower modification degrees compared to those of gels obtained at room temperature, supermacroporous chitosan cryogels with Young's moduli up to 90 kPa can be fabricated in one step. Investigations of chitosan cryogels biocompatibility in a mouse model have shown that a moderate inflammatory reaction around the implants is accompanied by formation of a normal granulation tissue. No toxic, immunosuppressive, and sensitizing effects on the recipient's tissues have been observed.