Increasingly restrictive environmental regulations for the maritime sector have led shipping companies to look for technological alternatives to reduce emissions. This article introduces a methodology to analyse emission reductions of ships in port by incorporating batteries into the ships or using an onshore power supply system. These have not yet been considered together for comparison or with a focus on ship operation. The aim is to avoid the use of auxiliary engines in ports. First, the cost calculation method to be used is specified; then, the engine’s behaviour and the established basic navigation criteria are analysed; and finally, different alternatives are considered. A methodology is afterwards defined for selecting alternatives, comparing their costs with those of using auxiliary engines in port. As an example, it is applied to a Ro-Ro route between the ports of Montoir (France) and Vigo (Spain). The results indicate that incorporating batteries into the ship produces greater savings in annual costs than onshore power supply. The cost savings from onshore power supply depend on the range of prices in each port. However, the greatest emission savings are obtained by using the onshore power supply. This methodology can be extrapolated to other routes and vessels by incorporating real operating data.