Buckwheat sprouts are a source of various nutrients, e.g., antioxidant flavonoids, which have a positive effect on human health. This study analyzed the content of phenolic compounds and assessed their impact on the antioxidant and anti-inflammatory properties and dietary fiber in modified buckwheat sprouts. For this purpose, the buckwheat seeds were modified by adding Saccharomyces cerevisiae var. boulardii. The modified buckwheat sprouts showed a higher content of total phenol compounds (1526 µg/g d.w.) than the control sprouts (951 µg/g d.w.) and seeds (672 µg/g d.w.). As a consequence, a higher antioxidant activity and anti-inflammatory effect were noted. Probiotic-rich sprouts also had the highest content of total dietary fiber and its soluble fraction. A correlation between phenolic compounds and the antioxidant and anti-inflammatory effects, as well as dietary fiber, was shown. The interaction between dietary fiber and phenolic compounds affects the bioaccessibility, bioavailability, and bioactivity of phenolic compounds in food. The introduction of probiotic yeast into the sprouts had a positive effect on increasing their nutritional value, as well as their antioxidant and anti-inflammatory activity. As a consequence, the nutraceutical potential of the raw material changed, opening a new direction for the use of buckwheat sprouts, e.g., in industry.