Dense molecular clouds in the Central Molecular Zone (CMZ) filling the $\sim$200 pc region around the Galactic Center (GC) allow to use gamma rays as tracers for cosmic rays (CRs). We present the updated analysis covering more than 100 hours of MAGIC observations of this region, which is believed to host a PeV proton accelerator. We use new analysis tools that were specially developed for such a task for computing the instrument responses, studying the morphology and extracting energy spectra of the extended gamma-ray emission. We observe no significant difference between the diffuse emission spectra of the immediate Galactic Center vicinity and the rest of the Galactic Ridge. Though the derived best fit CR profile is compatible with the 1/r radial distance scaling, we argue that this measurement is presently limited by the our knowledge of the gas distribution in 3D at the GC.