The use of Dutch dairy manure for biogas production is expected to increase from 10% in 2020 to 60% in 2030. Traditionally, manure is returned to fields as a source of nutrients and organic carbon. Since a share of manure carbon is converted into biogas, this practice impacts the organic carbon input to soil (OCIS) of the dairy farms. The magnitude of the impact depends on the magnitude of the other sources of organic carbon. This impact is not considered by current advocates for large-scale use of dairy manure for biogas while understanding it is essential because of the risk of decreasing carbon soil input. Therefore, a study of carbon flows of dairy farms that eventually contribute to the OCIS is required. In this paper, we use substance flow analysis to quantify the carbon flows on different Dutch dairy farms and investigate the impact of using manure for biogas production to their OCIS (kgC/year/ha). The farms differ in farming practices such as whether cows are grazed outside or not. The results show that about 40% of OCIS of a Dutch dairy farm comes from manure and the rest comes from its crop production. The organic carbon from manure to the soil is also limited by the need to export manure due to the Dutch nutrient regulations. The overall reduction in OCIS caused by biogas production is 10%–20%. The impact is largest in farms with no grazing. These findings provide insights into the possible trade-offs of using manure for biogas production.