In recent years, the air transport sector has played a significant role in the economy of the areas served. The demand for air travel has doubled every fifteen years and has grown faster with respect to other industries. This is also due to the introduction of low-cost airlines (LCA). In the coming decades, more efficient management of airports will become an essential aspect to address. A clear understanding of the current airport structure based on the analysis of the operational efficiency will therefore be necessary. All air carriers seek to expand their operations at airports, which tend to operate efficiently in order to reduce costs. However, in carrying out their activities and maximizing operational efficiency, airports should simultaneously manage to increase their passengers’ satisfaction. All over the world, passengers are demanding higher levels of service and regulators are paying increasing attention to the provision of airport services and the quality of the services supplied. Starting from these considerations, the aim of this paper is to study the efficiency of an airport through joint analysis of the operational efficiency (with the Data Envelopment Analysis -DEA-model) for the airport manager (by maximizing the exploitation of existing infrastructures), taking into consideration the quality of airport services as perceived by the user. The original and added value of this work lies in the quantitative analysis of the main characteristics that determine the efficiency of main European airports, also taking into account the quality perceived by the users during their trips with the air mode. Thus, the efficiency of 103 European airports in 37 different countries, for the year 2018, were compared, highlighting the effect of low-cost airlines. This aspect, as far as the authors know, has not been treated in the literature. Indeed, this study represents a decision support system (DSS) tool for operational managers in the air sector for the identification of the characteristics that improve airport efficiency. This paper refers to the pre-COVID-19 period because it would not be useful to make an efficiency analysis influenced by the pandemic, since the latter represents a specific event. Therefore, this analysis provides interesting inputs for both researchers and practitioners to manage the issue of efficiency in ordinary contexts. Moreover, the airline industry is characterized by cut-throat competition, and it may be very useful in the close future to examine this issue to improve firms’ management in the industry.