Monitoring microclimate variables within cities with high accuracy is an ongoing challenge for a better urban resilience to climate change. Assessing the intra-urban characteristics of a city is of vital importance for ensuring fine living standards for citizens. Here, a novel mobile microclimate station is applied for monitoring the main microclimatic variables regulating urban and intra-urban environment, as well as directionally monitoring shortwave radiation and illuminance and hence systematically map for the first time the effect of urban surfaces and anthropogenic heat. We performed day-time and night-time monitoring campaigns within a historical city in Italy, characterized by substantial urban structure differentiations. We found significant intra-urban variations concerning variables such as air temperature and shortwave radiation. Moreover, the proposed experimental framework may capture, for the very first time, significant directional variations with respect to shortwave radiation and illuminance across the city at microclimate scale. The presented mobile station represents therefore the key missing piece for exhaustively identifying urban environmental quality, anthropogenic actions, and data driven modelling toward risk and resilience planning. It can be therefore used in combination with satellite data, stable weather station or other mobile stations, e.g. wearable sensing techniques, through a citizens’ science approach in smart, livable, and sustainable cities in the near future.