Local and Regional Authorities require indicators at the intra-urban scale to design adequate policies to foster the achievement of the objectives of Sustainable Development Goal (SDG) 11. Updated high-resolution population density and settlement maps are the basic input products for such indicators and their sub-indicators. When provided at the intra-urban scale, these essential variables can facilitate the extraction of population flows, including both local and regular migrant components. This paper discusses a modification of the dasymetric method implemented in our previous work, aimed at improving the population density estimation. The novelties of our paper include the introduction of building height information and site-specific weight values for population density correction. Based on the proposed improvements, selected indicators/sub-indicators of four SDG 11 targets were updated or newly implemented. The output density map error values are provided in terms of the mean absolute error, root mean square error and mean absolute percentage indicators. The values obtained (i.e., 2.3 and 4.1 people, and 8.6%, respectively) were lower than those of the previous dasymetric method. The findings suggest that the new methodology can provide updated information about population fluxes and processes occurring over the period 2011–2020 in the study site—Bari city in southern Italy.