One of the challenges for network operators is to design and deploy cost-efficient transport networks (TNs) to meet the high capacity and strict latency/reliability requirements of today’s emerging services. Therefore, they need to consider different aspects, including the appropriate technology, the level of reconfigurability, and the functional split option. A crucial aspect of network design is assessing the impact of these aspects against the total cost of ownership (TCO), latency, and reliability performance of a given solution. For this reason, this paper proposes a framework to investigate the TCO, latency, and reliability performance of a set of fiber and microwave-based TN architectures. They are categorized based on their baseband functional split option and the reconfigurability capabilities of the equipment used. The results, based on real data from a non-incumbent operator, show that in most of the considered scenarios, a microwave-based TN exhibits lower TCO than a fiber-based one. The TCO gain may vary with the choice of the functional split option, geo-type, reconfigurability features, fiber trenching costs, and cost of microwave equipment, with a more significant impact in a dense urban geo-type, where for a low layer functional split option the fiber- and microwave-based architectures have a comparable TCO. Finally, it was found that the considered fiber and microwave architectures have almost similar average latency and connection availability performance. Both are suitable to meet the service requirements of 5G and beyond 5G services in most of the considered scenarios. Only in extreme latency-critical scenarios, a small number of the cells might not fully satisfy the latency requirements of a low layer split option due to multiple microwave hops in the microwave-based architecture.