Nitrous oxide (N2O) emissions from pastures can vary significantly depending on soil and environmental conditions, nitrogen (N) input, as well as the plant’s ability to take up the N. We tested the hypothesis that legume-based N sources are characterized by significantly lower emission factors than mineral N based dairy systems. Therefore, this study monitored N2O emissions for a minimum of 100 days and up to two growing seasons across a gradient of plant species diversity. Emissions were measured from both, grazed pastures and a controlled application of urine and dung using the static chamber method. About 90% of the accumulated N2O emissions occurred during the first 60–75 days. The average accumulated N2O emissions were 0.11, 0.87, 0.99, and 0.21 kg ha−1 for control, dung, urine patches, and grazed pastures, respectively. The N uptake efficiency at the excreta patch scale was about 70% for both dung and urine. The highest N2O-N emission factor was less than half compared with the IPCC default (0.3 vs. 0.77), suggesting an overestimation of N2O-N emissions from organically managed pastures in temperate climates. Plant diversity showed no significant effect on the N2O emissions. However, functional groups were significant (p < 0.05). We concluded that legume-containing pasture systems without a fertilizer addition generally appear capable of utilizing nitrogen inputs from excreta patches efficiently, resulting in low N2O emissions.