The European Union has set ambitious climate goals as part of its commitment to the Paris Agreement and the European Green Deal. Urban freight transport is one of the main sources of greenhouse gas emissions, air pollution, and traffic congestion, which is a major hurdle for sustainable urban development. Despite significant policy and research interest, there are currently limited published studies that fully combine rail freight transport with low/zero-emission last-mile delivery and its comprehensive economic evaluation. This study presents and evaluates a comprehensive solution combining rail transport of inter-regional shipments with logistics micro-hubs located near the railway station and transshipping shipments through environmentally friendly last-mile delivery modes such as electric vehicles, cargo bikes, or crowdshipping. The methodology consists of applying several methods, such as operational simulation and break-even analysis, to assess the economic viability of the proposed solution, through different scenarios for the evolution of the regulatory framework (in particular, transport emission allowances). The findings indicate that carbon pricing significantly increases the cost of road regional deliveries by Heavy Goods Vehicle, while rail-integrated models demonstrate relative stability. A modal shift of 40% from road to rail reduced monthly freight emissions by approximately 25%, primarily by eliminating long-distance Heavy Goods Vehicle trips with a low-carbon rail section. Moreover, the combined rail–bike system offered the most cost-efficient and environmentally robust configuration under emission trading system conditions, reinforcing the strategic value of multimodal urban freight systems. The research provides evidence-based insights for policymakers, logistics operators, and urban planners, highlighting the role of rail-integrated, multimodal systems in shaping sustainable and resilient urban freight networks.