Disclosed are various approaches for secure inter-application communication with unmanaged applications using certificate enrollment. A certificate signing request can be received from an unmanaged application via an inter-application communication method supported by an operating system of a computing device, and an identity of the unmanaged application can be verified. The certificate signing request can be provided to a certifying authority, and a certificate can be received from the certifying authority. The certificate can be provided to the unmanaged application.