Aims. We investigate the vector magnetic field and Doppler velocity in the photosphere and upper chromosphere of a young emerging flux region of the sun close to disk center. Methods. Spectropolarimetric scans of a young active region made using the second generation Tenerife Infrared Polarimeter (TIP II) on the German Vacuum Tower Telescope (VTT) are analyzed. The scanned area contained multiple sunspots and an emerging flux region. An inversion based on the Milne-Eddington approximation was performed on the full Stokes vector of the chromospheric He I 10 830 Å and the photospheric Si I 10 827.1 Å lines. This provided the magnetic vector and line-of-sight velocity at each spatial point in both atmospheric layers. Results. A clear difference is seen between the complex magnetic structure of the emerging flux region (EFR) in the photosphere and the much simpler structure in the upper chromosphere. The upper chromospheric structure is consistent with a set of emerging loops following elongated dark structures seen in the He I 10 830 Å triplet, similar to arch filament systems (AFS), while in the photosphere we infer the presence of U-loops within the emergence zone. Nonetheless, in general the upper chromospheric field has a similar linear relationship between inclination angle and field strength as the photospheric field: the field is weak (≈300 G) and horizontal in the emergence zone, but strong (up to 850 G) and more vertical near its edges. The field strength decreases from the photosphere to the upper chromosphere by approximately 0.1-0.2 G km −1 (or even less) within the emergence zone and by 0.3-0.6 G km −1 in sunspots located at its edge. We reconstructed the magnetic field in 3D based on the chromospheric vector field under the assumption that the He I 10 830 Å triplet forms along the magnetic field loops. The reconstructed loops are quite flat with supersonic downflows at both footpoints. Arguments and evidence for an enhanced formation height of He I 10 830 Å in arch-filaments seen in this line are provided, which support the validity of the reconstructed loops. Conclusions. The main chromospheric properties of EFRs previously deduced for a single region NOAA 9451 are shown to be valid for another region as well, suggesting that the main original results may have a wider application. The main exception is that only the first region displayed a current sheet in the chromosphere. We propose a scenario in which the relatively complex photospheric structure evolves into the simpler chromospheric one.