Quantifying soil organic carbon stocks (SOC) is a critical task in decision support related to climate and land management. Carbon inputs in soils are affected by development of belowground (BGB) and aboveground (AGB) biomass. However, uncertain fixed values of root:shoot ratios (R/S) are widely used for calculating SOC inputs in agroecosystems. In this study, we 1) assessed the effect of harvest frequency (zero, one, two, and five times annually) on the root and shoot development of the perennial grasses Phalaris arundinacea (RCG), Festuca arundinacea (TF), and Festulolium (FL); 2) determined the effect of management on the carbon and nitrogen content in AGB and BGB; and 3) assessed the implications of R/S for SOC quantification. We found the highest yields of BGB in zero-cut treatments with 59% (FL)–70% (RCG) of total biomass. AGB yield was highest in the five-cut treatments with 54% (RCG)–60% (FL), resulting in a decreasing R/S with frequent management, ranging from 1.6–2.3 (zero cut) to 0.6–0.8 (five cuts). No differences in R/S between species were observed. Total carbon yield ranged between 5.5 (FL, one cut) and 18.9 t ha−1 year−1 (FL, zero cut), with a higher carbon content in AGB (45%) than BGB (40%). We showed that the input of total organic carbon into soil was highest in the zero-cut treatments, ranging between 6.6 and 7.6 t C ha−1 year−1, although, in the context of agricultural management the two-cut treatments showed the highest potential for carbon input (3.4–5.4 t C ha−1 year−1). Our results highlighted that using default values for R/S resulted in inaccurate modeling estimations of the soil carbon input, as compared to a management-specific application of R/S. We conclude that an increasing number of annual cuts significantly lowered the R/S for all grasses. Given the critical role of BGB carbon input, our study highlights the need for comprehensive long-term experiments regarding the development of perennial grass root systems under AGB manipulation by harvest. In conclusion, we indicated the importance of using more accurate R/S for perennial grasses depending on management to avoid over- and underestimation of the carbon sink functioning of grassland ecosystems.