The existence of road infrastructure such as bridges that do not meet current design criteria, the deterioration of these due to use, environmental factors and extraordinary or unforeseen conditions, and the increase in seismic and gravitational design loads due to regulatory updates, generate the need for search of new design and retrofitting alternatives for this type of structure. Thus, the conditions of these structures need to be assessed and corresponding interventions need to be identified. It is important to implement alternatives that are both economically and functionally efficient. For example, base isolation can reduce direct construction costs by using devices designed and built in the country of origin, but the unfamiliarity and importation costs of these devices are the main obstacles to mass use. In this article, a comparative analysis is performed of a conventional design and an integrated design for base isolation using low-cost unbonded fiber-reinforced elastomeric isolators (U-FREIs) made in Colombia. A methodology is proposed for the analysis of new and existing isolated structures, in which the isolators are placed between the substructure and superstructure. This methodology is used to design and strengthen a typical prestressed concrete girder bridge, and the results are compared against those obtained using a conventional scheme. Finally, an existing bridge is analyzed using on-site measurements to determine the dynamic properties and modify the numerical model used for analysis, design, and retrofitting. The effectiveness of the proposed methodology as a tool for the design of new bridges and the retrofitting of existing structures was verified for all cases. Economic and structural benefits were evidenced by reductions in direct costs of up to 15% and the seismic force of up to 20%, respectively.