Context. High-resolution very long baseline interferometry (VLBI) observations of NGC 1052 show a two sided jet with several regions of enhanced emission and a clear emission gap between the two jets. This gap shrinks with increasing frequency and vanishes around ν ∼ 43 GHz. The observed structures are due to both the macroscopic fluid dynamics interacting with the surrounding ambient medium including an obscuring torus and the radiation microphysics. In order to model the observations of NGC 1052 via state-of-the art numerical simulations both the fluid-dynamical and emission processes have to be taken into account. Aims. In this paper we investigate the possible physical conditions in relativistic jets of NGC 1052 by directly modelling the observed emission and spectra via state-of-the-art special-relativistic hydrodynamic (SRHD) simulations and radiative transfer calculations. Methods. We performed SRHD simulations of over-pressured and pressure-matched jets using the special-relativistic hydrodynamics code Ratpenat. To investigate the physical conditions in the relativistic jet we coupled our radiative transfer code to evolutionary algorithms and performed simultaneous modelling of the observed jet structure and the broadband radio spectrum. During the calculation of the radiation we consider non-thermal emission from the jet and thermal absorption in the obscuring torus. In order to compare our model to VLBI observations we take into account the sparse sampling of the u-v plane, the array properties and the imaging algorithm. Results. We present for the first time an end-to-end pipeline for fitting numerical simulations to VLBI observations of relativistic jets taking into account the macro-physics including fluid dynamics and ambient medium configurations together with thermal and non-thermal emission and the properties of the observing array. The detailed analysis of our simulations shows that the structure and properties of the observed relativistic jets in NGC 1052 can be reconstructed by a slightly over-pressured jet (d_k ∼ 1.5) embedded in a decreasing pressure ambient medium