A recurrent behavioral trait model to study adaptation to urban environments is the flight initiation distance (FID), measured as the distance at which animals flee from an approaching threat. It has previously been shown that urban birds display shorter FID than their non-urban (rural) counterparts. However, discerning whether this is the result of habituation to human presence and frequentation, or of ecological factors related to the size of the city (considered as “systemic habituation”), has not yet been addressed. In this study, we analyzed House Sparrow (Passer domesticus) FIDs in a network of 26 small towns and villages within the same region in northeastern Spain. Our aim was to relate FID to human population density and settlement size. If the habituation to human presence hypothesis was supported, we should expect FIDs to decrease with the density of the human population across the human settlements, since this type of habituation is related to the rate of human exposure and this is proportional to human density. However, if the systemic habituation hypothesis was supported, FIDs should instead relate to the size of the human settlements, as the abundance of predators, similarly to other ecological variables, is often proportional to the size of towns. Results showed House Sparrows to be bolder in larger human settlements, but not necessarily the ones with a higher density of human population. This supports the idea that the fact that urban birds display shorter FIDs than their rural counterparts is the result of systemic ecological factors rather than the results of a simple habituation to humans.