Collagen is a widely studied natural polymer for use as a scaffold material for various tissue engineering applications. Untreated collagen, however, has a fast biodegradation rate and low mechanical strength. Additionally, collagen cross-linking has been studied extensively and different cross-linking agents and methods have been explored. Although glutaraldehyde (GA) is the most convenient and traditional chemical agent currently used for this purpose, it nevertheless poses potential cytotoxicity. Therefore, 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) is widely being studied as well, due to its characteristic of being a zero-length cross-linker that does not remain in the collagen's structure. Nevertheless, cross-linking with EDC can be implemented in several ways. In this study, two methods of cross-linking with EDC, prior to and post freeze-drying, were examined for freeze-dried collagen scaffolds. Four different collagen concentrations between 0.3 and 2.0 w% were inspected and different cross-linking methods were examined by a differential scanning calorimeter (DSC) to determine the collagen's denaturation temperature (T_d). Furthermore, the water uptake abilities of the scaffolds were tested in phosphate buffered saline (PBS) and the scaffolds’ pore structure was examined with a scanning electron microscope (SEM). As assumed, the DSC measurements demonstrated that collagen T_d values increased with increasing collagen concentration. With lower collagen concentrations, the cross-linking post freeze-drying enhanced the T_d values, but with higher collagen concentrations, the T_d values were increased only with cross-linking prior to freeze-drying. The water uptake measurement showed increased water uptake ability when cross-linking post freeze-drying. The pore sizes of the different collagen scaffolds were between 50 and 120 μm.