Ovarian failure, hormonal disorders, and side effects of cancer treatments are some underlying causes that can affect a woman’s ability to conceive. Given this concern, different preventive options arise to preserve fertility such as cryopreservation of embryos, oocytes, and ovarian tissue; however, they have significant limitations. Currently, bioengineering allows the adoption of different strategies against reproductive disorders and that is why this study evaluates the first step to manufacture in vitro decellularized ovarian bioscaffolds based on the specific ECM of ovarian tissue. To this end, complete rat ovaries have been used that have been subjected to four decellularization protocols that combine different mechanical-chemical-enzymatic treatments in order to eliminate cell nuclei, while maintaining the macro and microstructure of the native tissue. The results of this study, of a histological and histochemical nature, have not revealed significant data regarding the elimination of cell nuclei. However, a novel protocol was identified that has generously removed some of the cellular material while preserving a good ECM structure. All this supports the idea of the importance of the selection of decellularizing agents and their respective concentrations; with special emphasis on the concentration of the strongest ionic detergents such as SDS and the effect it causes on the samples. In addition, what has already been revealed in recent studies has been confirmed, which is that the ovarian scaffolds generated with SDC have been able to better preserve the extracellular composition, which could be beneficial for recellularization and other applications. These generated bioscaffolds form a promising basis for future experiments where the objective should be to optimize the protocols and conduct additional studies.