The expansion of the Internet of Moving Things (IoMT) leads to limitless and continuous working playgrounds exploited by highly dynamic end devices. This requires the adoption of multi-Radio Access Technologies (RATs)-based strategies to provide IoMT units with ubiquitous connectivity. To this end, the development of secure bootstrapping and authentication mechanisms is necessary to permit the secure operation of end devices. Given the transmission and power limitations of these elements, current cryptographic solutions do not address these stringent requirements. For that reason, in the study we present a Multi-Access Edge Computing (MEC)-based end-to-end architecture that enables an efficient and secure authentication and key agreement between end devices and network servers over heterogeneous resource-limited networks such as the Low Power Wide Area Networks (LPWANs). Our proposal is based on the Authentication, Authorization, and Accounting (AAA) architecture and the recent Internet Engineering Task Force initiatives Static Context Header Compression and Low-Overhead CoAP-EAP. The results obtained from experimental tests reveal the validity of the proposal as it enables constrained IoMT devices to gain IPv6 connectivity as well as performs end-to-end secure authentication with notable reliability and controlled latency.