Nanoscale phase separation was induced in the K-doped RuCl₃ van der Waals material by annealing, and studied with the goal to find a natural design strategy for the formation of two-dimensional architectures as an alternative to the costly and time-consuming experimental artificial growth methods. Phase conversion was traced by means of thermogravimetric analysis combined with mass spectrometry. The local crystal structure of co-existing K₃Ru₂Cl₉ domains with the sizes of about 100 nm was solved by 3D electron diffraction.