The AIFIRA (Applications Interdisciplinaires des Faisceaux d'Ions en Région Aquitaine) ion beam facility at the CENBG (Centre d'Etudes Nucléaires de Bordeaux-Gradignan) is being equipped with a high demagnification focused microbeam line. This beam line, which is under its final stage of development, should allow focusing of protons and alpha particles down to a sub-micrometer resolution, and is therefore referred to as a “nanobeam line” in the following paper. We present the complete beam transport simulation along the chosen configuration for the nanobeam line, which consists of a long working distance doublet-triplet of Oxford Microbeam Ltd. OM-50® quadrupoles. These simulations have been performed using the Geant4 Monte Carlo simulation toolkit, which has been previously validated for ray-tracing studies in the design of quadrupole microbeam systems. They include a fine modelling of the quadupole magnetic field, based on the analytical Enge's model, which is compared to a classical square field model and to a high granularity tri-dimensional field map computed with the OPERA3D® software. The beam emittance model is parameterized from experimental measurements performed directly on the HVEE Singletron® at the AIFIRA facility, allowing the computation of the beam transmitted current along the nanobeam line. Grid shadow images, acquired from simulations, for system alignment purposes and beam deflection studies on target are presented as well.