Techniques for managing certificates in segregated networks are disclosed. One example technique includes upon receiving executable instructions of a software application and a reference table containing entries of reference objects in the software application, identifying a digital certificate independently obtained by the segregated network for each of the reference objects. The method also includes generating a mapping table having entries individually identifying the reference objects and data representing the digital certificates. The method further includes deploying for execution to one or more of the servers in the segregated network, the software application along with the generated mapping table. During execution, the software application can dereference one of the reference objects to locate one of the digital certificates in in the generated mapping table corresponding to one of the reference objects.