A mobile device may include at least one memory and a processor-cooperating with the at least one memory to enroll with an enterprise mobility management (EMM) server and store a plurality of different managed enterprise applications in the at least one memory, and receive and store a digital certificate associated with a given one of the managed enterprise applications in a secure shared location within the at least one memory. The processor may further run the plurality of managed enterprise applications to share access to the digital certificate from the secure shared location and generate and send encrypted data to another mobile device via the EMM server with all of the managed enterprise applications using the same digital certificate associated with the given managed enterprise application for encryption so that the EMM server is unable to decrypt the encrypted data.