Fabrication of Ytterbium-doped active fibers with different designs, compositions and high Yb concentration has attracted an intense interest. For making highly Yb-doped fibers, co-dopants like phosphorous (P) and aluminum (Al) are also employed in order to modify refractive index and increase Yb solubility, avoiding clusters and phase segregations. Indeed, Yb-clustering results in quenching effects and increased propagation losses due to energy transfer between clustered ions. Therefore, the chemical composition and phase homogeneity of the fiber core have key influences on the performance of an active fiber. However, conventional fabrication techniques such as MCVD (modified chemical vapor deposition) and OVD (outside vapor deposition) are approaching the limit. In this contribution, we have developed an approach for fabrication of such active fibres based on granulated silica derived from the sol-gel process. The advantage of this method is the fabrication of active fibers with high dopant contents and homogeneity. Here, using high angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) in atomic scale, we report the direct, nano-scale and atomic-resolution observation of individual Yb dopant and co-dopant (i.e. Al, P) atoms for different fabricated fibers. The chemical mapping from STEM-EDX shows an extremely homogeneous distribution of the dopants and co-dopants in nano-scale for our fabrication protocol. However in atomic resolution, we also identified the possible Yb clusters in the range of 10 atoms within the core structure. The size, structure, and distribution of these clusters are determined with an Yb-atom detection efficiency of almost 100% by STEM.