This study examined the potential of using the endophytic bacteria Bacillus subtilis (10-4 and 26D) to enrich hydroponically grown potato seed minitubers (Solanum tuberosum L. cv. Bashkirsky) to improve plant growth, photosynthetic pigments, yield, and quality parameters, including nutritional value (i.e., macro-/microelements, vitamin C, anthocyanins). Potato seed minitubers, obtained from in-vitro-grown microplants in a hydroponic system, were inoculated with endophytic B. subtilis and subsequently grown in pots under controlled conditions. The results demonstrated the successful colonization of seed minitubers by B. subtilis, with subsequent distribution into growing plants (roots, shoots). The endophytes accelerated the plant’s phenological shifts, resulting in earlier emergence of sprouts, budding, and flowering compared with control plants. They also had increased leaf photosynthetic pigments (chlorophyll (Chl) a, Chl b, and carotenoids), total leaf area, and positively influenced leaf proline contents. The height of plants and number of stems per plant did not change significantly upon endophyte treatment, but improved root growth was observed throughout the experiment. As a result of endophyte application, there was an increase in stolon weight, number and size of tubers, and overall tuber yield. There were no significant differences in terms of total dry matter and starch content of the tubers compared to the control group, but the sugar levels decreased and the size of the starch grains was larger in endophyte-treated tubers. Furthermore, endophyte treatment resulted in an increased accumulation of nutrients including N, P, K, Cu, and Fe, as well as vitamin C and anthocyanins in harvested tubers. These findings indicate that colonization of hydroponically grown potato seed minitubers with endophytic B. subtilis (10-4 and 26D) before planting has great potential as an eco-friendly approach to obtain higher-quality seeds and to increase tuber yield and nutritional value in field conditions.