We describe the bottom-up module of the High-Elective Resolution Modelling Emission System version 3 (HERMESv3), a python-based and multiscale modelling tool intended for the processing and computation of atmospheric emissions for air quality modelling. HERMESv3 is composed of two separate modules: the <i>global_regional</i> module and the <i>bottom_up</i> module. In a companion paper (Part 1, Guevara et al., 2019) we presented the <i>global_regional</i> module. The <i>bottom_up</i> module described in this contribution is an emission model that estimates anthropogenic emissions at high spatial (e.g. road link level) and temporal (hourly) resolution using state-of-the-art calculation methods that combine local activity and emission factors along with meteorological data. The model computes bottom-up emissions from point sources, road transport, residential and commercial combustion, other mobile sources and agricultural activities. The computed pollutants include main criteria pollutants (i.e. NO<sub>x</sub>, CO, NMVOC, SO<sub>x</sub>, NH<sub>3</sub>, PM<sub>10</sub> and PM<sub>2.5</sub>) and greenhouse gases (i.e. CO<sub>2</sub> and CH<sub>4</sub>, only related to combustion processes). Specific emission estimation methodologies are provided for each source, and are mostly based on (but not limited to) the calculation methodologies reported by the European EMEP/EEA air pollutant emission inventory guidebook. Meteorological-dependent functions are also included to take into account the dynamical component of the emission processes. The model also provides several functionalities for automatically manipulating and performing spatial operations on georeferenced objects (shapefiles and raster files). The model is designed so that it can be applicable to any European country/region where the required input data is available. As in the case of the <i>global_regional</i> module, emissions can be estimated on several user-defined grids, mapped to multiple chemical mechanisms and adapted to the input requirements of different atmospheric chemistry models (CMAQ, WRF-Chem and MONARCH) as well as a street-level dispersion model (R-LINE). Specific emission outputs generated by the model are presented and discussed to illustrate its capabilities.