Sustainable urban resource management depends essentially on a sound understanding of a city’s resource flows. One established method for analyzing the urban metabolism (UM) is the Eurostat material flow analysis (MFA). However, for a comprehensive assessment of the UM, this method has its limitations. It does not account for all relevant resource flows, such as locally sourced resources, and it does not differentiate between flows that are associated with the city’s resource consumption and resources that only pass through the city. This research sought to gain insights into the UM of Amsterdam by performing an MFA employing the Eurostat method. Modifications to that method were made to enhance its performance for comprehensive UM analyses. A case study of Amsterdam for the year 2012 was conducted and the results of the Eurostat and the modified Eurostat method were compared. The results show that Amsterdam’s metabolism is dominated by water flows and by port-related throughput of fossil fuels. The modified Eurostat method provides a deeper understanding of the UM than the urban Eurostat MFA attributed to three major benefits of the proposed modifications. First, the MFA presents a more complete image of the flows in the UM. Second, the modified resource classification presents findings in more detail. Third, explicating throughput flows yields a much-improved insight into the nature of a city’s imports, exports, and stock. Overall, these advancements provide a deeper understanding of the UM and make the MFA method more useful for sustainable urban resource management.