Biogas production on dairy farms is promoted as a climate change measure since it captures methane, a greenhouse gas emitted by manure, and produces renewable energy. Digestate is a by-product of biogas production and is often used for nutrient recycling in a similar way as traditional manure. Despite having similar functions, manure and digestate have different behaviors related to nitrogen recycling and nitrogen emissions which are significant agricultural and environmental concerns of manure. This paper provides an insight into the impact of biogas production on nitrogen emissions and nitrogen recycling issues of the current dairy farming practice. Using the Substance Flow Analysis (SFA) approach, we analyzed the changes on three levels: manure handling, dairy farm, and the whole chain. Four biogas production options on a Dutch dairy farm related to types and sources of feedstocks were considered. We quantified biogas output, nitrogen fertilizer replacement percentage (%) and consequential nitrogen emissions (kgN/year; kgN/m(3) biogas produced) of these productions in comparison with the baseline of current dairy farming without biogas. We conclude that biogas production options with additional feedstocks will cause profound changes in the nitrogen recycling on dairy farms and the nitrogen emissions at the chain level. Besides, the results show that determining the optimal biogas production option can be challenging as the evaluation is highly dependent on the used nitrogen indicator and the included level of analysis. Our findings show how SFA and a multilevel perspective can give a broader understanding of environmental trade-offs.