The proposed sectorial and national-sectorial emissions accounting methods for the PyPSA-Eur-Sec model adds a layer of abstraction to the model that allows decarbonisation at defined rates of individual sectors. PyPSA-Eur-Sec is a sector-coupled energy model of the European energy system and includes the electricity, heating, transportation, and industry sectors. The model and this extension are fully open-source, and all data sources and cost assumptions are openly available. The model allows for transparent, reliable, and computationally efficient analyses. These can form a solid basis for energy investments and policy advice. Additionally, for the first time, we present a diagram of the inner workings of the PyPSA-Eur-Sec model. We visualise exactly the possible energy flows, energy conversions, and couplings between the sectors in the model.•Future cost-optimal European energy system configurations can be obtained from the PyPSA-Eur-Sec model under a given carbon dioxide emission budget.•This model extension allows steering the emissions individually in the four modelled sectors electricity, heating, transportation, and industry.•We provide a visual overview of the energy flows and conversions optimised in the model.