During the last few years, scientists have become increasingly concerned about air quality. Particularly in large cities and industrialised areas, air quality is affected by pollution from natural and anthropogenic sources and this has a significant impact on human health. Continuous monitoring of air quality is an important step in investigating the causes and reducing pollution. We propose a new autonomous multi-rotor aerial platform that can be used to perform real-time monitoring of air quality in large cities. The air quality monitoring system is able to cover large areas, with high spatial resolution, even above average buildings, while being relatively low cost. We evaluate the proposed system in several locations throughout a metropolitan city, during different seasons and generate fine-grained heat-maps that display the level of pollution of specific areas based on different altitudes.