The magnetic field structure of sunspots above the photosphere remain poorly understood due to limitations in observations and the complexity of these atmospheric layers. In this regard, we studied the large isolated sunspot (70”× 80”) located in the active region NOAA 12546 with spectro-polarimetric measurements acquired along the Fe I 617.3 nm and Ca II 854.2 nm lines with the IBIS/DST instrument, under excellent seeing conditions lasting more than three hours. Using the Non Local Thermodynamic Equilibrium inversion code we inverted both line measurements simultaneously to retrieve the three-dimensional magnetic and thermal structure of the penumbral region from the bottom of the photosphere to the middle chromosphere. The analysis of data acquired at spectral ranges unexplored allow us to show clear evidence of the spine and intra-spine structure of the magnetic field at chromospheric heights. In particular, we found a peak-to-peak variations of the magnetic field strength and inclination of about 200 G and 10° chromospheric heights, respectively, and of about 300 G and 20° in the photosphere. We also investigated the structure of the magnetic field gradient in the penumbra along the vertical and azimuthal directions, confirming previous results reported in the literature from data taken at the spectral region of the He I 1083 nm triplet.