- Owing to the individuality of intermetallic compounds, they are regarded as a special class of materials. As such, there is a need to develop a step‐by‐step methodology for solution of their structure. The current paper adapts the methodology of structure solution from precession electron diffraction (PED) zonal data for intermetallics. The optimization of PED parameters for structure determination was achieved through the development of the atomic model of a well known Mg17Al12 (β) intermetallic phase. It was concluded that the PED acquisition parameters, the number of unique reflections and the quality of the merging process are the most important parameters that directly influence the correctness of a structure solution. The proposed methodology was applied to the structure solution of a highly complex new Mg48Al36Ag16 phase, which was recently revealed in the Mg–Al–Ag system. The final atomic model consisted of 152 atoms in the unit cell, distributed over 23 unique atomic positions. The correctness of the atomic model was verified by the reasonability of the interatomic distances and coordination polyhedra formed. It was found that the experimental model of Φ‐Al17.1Mg53.4Zn29.5 can be assigned as a structure type for the Mg48Al36Ag16 phase. The Δ value, which measures the similarity between two structures, was calculated as 0.040.