The present paper pertains to mechanical properties and structure of nanocrystalline multiferroic BeFiO3 (BFO) thin films, grown by atomic layer deposition (ALD) on the Si/SiO2/Pt substrate. The usage of sharp-tip-nanoindentation and multiple techniques of structure examination, namely, grazing incidence X-ray diffraction, X-ray photoelectron spectroscopy, scanning electron microscopy, and energy dispersive X-ray spectrometry, enabled us to detect changes in elastic properties (95 GPa ≤ E ≤ 118 GPa) and hardness (4.50 GPa ≤ H ≤ 7.96 GPa) of BFO after stages of annealing and observe their relation to the material's structural evolution. Our experiments point towards an increase in structural homogeneity of the samples annealed for a longer time. To our best knowledge, the present report constitutes the first disclosure of nanoindentation mechanical characteristics of ALD-fabricated BeFiO3, providing a new insight into the phenomena that accompany structure formation and development of nanocrystalline multiferroics. We believe that our systematic characterization of the BFO layers carried out at consecutive stages of their deposition provides pertinent information which is needed to control and optimize its ALD fabrication.