Animal biodiversity in cities is generally expected to be uniformly reduced, but recent studies show that this is modulated by the composition and configuration of Urban Green Areas (UGAs). UGAs represent a heterogeneous network of vegetated spaces in urban settings that have repeatedly shown to support a significant part of native diurnal animal biodiversity. However, nocturnal taxa have so far been understudied, constraining our understanding of the role of UGAs on maintaining ecological connectivity and enhancing overall biodiversity. We present a well-replicated multi-city study on the factors driving bat and nocturnal insect biodiversity in three European cities. To achieve this, we sampled bats with ultrasound recorders and flying insects with light traps during the summer of 2018. Results showed a greater abundance and diversity of bats and nocturnal insects in the city of Zurich, followed by Antwerp and Paris. We identified artificial lighting in the UGA to lower bat diversity by probably filtering out light-sensitive species. We also found a negative correlation between both bat activity and diversity and insect abundance, suggesting a top-down control. An in-depth analysis of the Zurich data revealed divergent responses of the nocturnal fauna to landscape variables, while pointing out a bottom-up control of insect diversity on bats. Thus, to effectively preserve biodiversity in urban environments, UGAs management decisions should take into account the combined ecological needs of bats and nocturnal insects and consider the specific spatial topology of UGAs in each city.