Nuclear safety, security, and safeguards (nuclear 3S) are essential components for establishing robust nuclear environments. Nuclear safety is to protect public and environments from radioactive contamination, which can be caused in accidents. Nuclear security is to protect nuclear facilities from terrorism or sabotage, which related to physical a ttacks or insider threats. And nuclear safeguards is to protect nuclear materials from extortion by a state with a purpose of weaponizing activities. When a new nuclear facility is introduced, it is possible to save abundant amount of resources by considering nuclear 3S in an early stage (design phases). Initially, the international atomic energy agency (IAEA) recommended safeguards-by-design (SBD) approach. The concept of SBD gradually expands to nuclear 3S-by-design (3SBD). Though there are differences in purpose and target subject, each nuclear ‘S’ is closely related with others. When introducing a certain technology or equipment in order to enhance one ‘S’, another ‘S’ also get affected. The effect can be synergies or conflicts. For instance, confidential information in nuclear security is required for a safeguards activity. On the contrary, inspection equipment for safeguards can be used for security. Pyroprocessing is a technology for managing used nuclear fuels. As pyroprocessing is a backend fuel cycle technology, a sensitive nuclear technology, safeguards has taken a large portion of nuclear 3S research in an effort to achieve international credibility and nuclear transparency. As mentioned, there are both synergies and conflicts in integrating nuclear 3S. In this study, we investigate potential challenges in applying nuclear 3S integration to pyroprocessing by addressing synergies and conflicts. This approach will suggest required supplementary methods to build the reliable pyroprocessing environment.