Waste management on small islands does not hold any straightforward solutions. The numerous difficulties include limited space availability, restricted recycling and resale opportunities and impacts on the local environment that become magnified particularly when the island is small-sized, densely populated and tourist dependent. The well-documented impact on the local environment includes resource loss, damage to the marine and local environment and continuous nuisances created by littering, trucks and treatment facilities. However, waste management can leave its mark beyond the local borders. The generation and treatment of waste is in fact gaining attention in its connection with greenhouse gas emissions (GHG). Although in the past GHG emissions were mainly associated with energy generation, today it is frequently acknowledged that improved waste management can also mitigate these emissions. This research paper analysis the flows involved in the management of municipal waste (MW) from an island perspective. Focusing on the island of Malta, which consists of 316 km2 and sustains a population density of 1327 people/km2, a Material Flow Analysis together with a carbon footprint is presented for 2012. The same analysis is then made for three prospective scenarios proposed in the Waste Management Plan for the Maltese Islands 2014–2020 using projected 2018 data. With the use of STAN 2.5 (SubSTance Flow ANalysis), a tabled down analysis of the collection, treatment and disposal/export flows involved in the management of Municipal Waste in Malta is presented. The flows are then translated into a carbon footprint analysis using CO2ZW® (a carbon footprint tool for waste management). The objective is to emphasize the relationship between GHG remove GHG and replace with Greenhouse Gas emissions and existing waste management flows and how this relationship changes when different collection, treatment and disposal options are selected. The research’s ultimate aim is therefore to underline the importance of placing climate concerns in waste management policies. The results note that, in terms of carbon emissions, Malta stands to benefit from the introduction of a second Mechanical Biological Treatment plant since carbon emissions will experience an extensive reduction from the 2012 estimates. However, further reduction of carbon emissions should be accompanied by the increase of dry material recycling, separate organic collection and an analysis of the current collection system particularly route optimisation.