This cytogenetic study evaluates the biostimulation potential of the aqueous extract of seabuckthorn fruits (AESF) in plant cells, using the Allium cepa species as a test plant. The effects were monitored both at the macroscopic and microscopically level. The onion bulbs were exposed to the action of different concentrations of AESF (0.5, 1, 1.5, 2, and 2.5%) for 72 h. The obtained results showed the positive effect induced by the aqueous extract on the growth of the meristematic roots, but only at concentrations ranging between 0.5–1.5%, when the average length of the roots had values between 2.51–3.40 cm, which means an increase compared to the untreated control with 3.71–40.49%. Within the same concentration range of the AESF, an effect of intensifying the mitotic activity was recorded. On the other hand, at the 2–2.5% concentration of the AESF, there was an inhibitory effect on the growth of meristematic roots. Additionally, concentrations ≥2% of AESF induced a cytotoxic and genotoxic effect through the occurrence of some chromosomal and nuclear abnormalities in A. cepa cells (sticky, laggards, ring chromosomes, and micronucleus). The obtained results suggest the biostimulation potential of the AESF for plant cells and the possibility of using it as an eco-friendly fertilizer.