In this paper, we present an optimisation integrated energy system model (IESA-Opt) for the Netherlands with the use of a linear programming formulation. This state-of-the-art model represents a scientific contribution as it integrates a European power-system model with a complete sectoral representation of the energy system technologies and infrastructure that account for all greenhouse gas emissions considered in the targets, and takes into consideration a detailed description of the cross-sectoral flexibility (e.g. flexible heat and power cogeneration, demand shedding from power-to-X and electrified industrial processes, short- and long-term storage of diverse energy carriers, smart charging and vehicle-to-grid for electric vehicles, and passive storage of ambience heat for the built environment). This model provides a detailed description of the operation of technologies and considers exogenous technological learning to simultaneously solve multi-year planning of investments, retrofitting, and economical decommissioning with intra-year operational, flexible, and despatch decisions. The model is applied to a case study of the Netherlands energy transition under the current climate policy and conservative projections for the economy and availability of resources. The results present a significant reliance on renewable energy sources, such as wind (800 PJ) and solar (300 PJ), to fuel the electrification revolution as well as biomass (550 PJ) for feedstock and heat purposes coupled with carbon capture, utilisation, and storage (CCUS) to achieve negative emissions in certain sectors. However, oil (880 PJ) and gas (1050 PJ) constitute almost half of the final energy demand as they are required for heat applications, industrial feedstock, refined oil products for export, and international transport fuel. Four different sensitivity analyses are presented for the emission reduction target, oil demand streams, biomass availability, and demand volumes. The most significant findings are as follows: 1) it is crucial to ...