Evaluating the net ecosystem carbon balance (NECB) of legume-based grasslands is crucial for optimizing grassland management and assessing the sustainability of the milk and beef industries. This study investigated the NECB of a boreal legume grassland in eastern Finland from May 2017 to May 2020, covering the entire three-year rotation cycle. We found that the grassland showed interannual variability in carbon sequestration, fixing 220 g C m−2 in the first year, 334 g C m−2 in the second year, and losing 146 g C m−2 in the last year during the grassland renewal period. The study also examined the effects of mineral nitrogen fertilizer and digestate residue addition on the NECB of the grassland. No significant differences in net ecosystem carbon dioxide exchange were observed between the two treatments, but the application of digestate slurry increased the NECB, suggesting that organic fertilizers could potentially enhance carbon sequestration and sustain ecosystem services. In conclusion, our findings emphasize the importance of developing climate-friendly renovation management practices that maximize the photosynthetic period in boreal legume grasslands. These practices, combined with the use of organic fertilizers, can contribute to improved carbon sequestration and support the sustainability of milk and beef industries that rely on grasslands.