Diets reliant on grazed, temperate herbage are prone to greater nitrogen (N) losses via urine than balanced stall-fed diets which poses a greater risk for N emissions. Measures for improving the N utilisation in grazing-based dairy cattle systems are predominantly investigated on homogenous clover-ryegrass pastures with high herbage yields and nutritional quality. In contrast, grazing-based systems reliant on less external inputs (e.g., synthetic fertilisers or concentrates) using semi-natural grassland as main feed source, such as in large parts of Central Europe, received less attention. The N utilisation and excretion of grazing cows in low-input dairy farms was, thus, investigated on nine commercial organic dairy farms in South Germany across one to four periods per farm. The dataset captured a diverse set of dairy production systems comprising 323 individual animal observations. A mean (± one standard deviation) milk production, DM intake (DMI), and pasture DMI of 23.9 kg (± 5.35), 21.0 kg (± 3.21), and 11.3 kg/d (± 4.83), respectively, was determined using titanium dioxide and faecal crude protein concentration as markers of faecal excretion and diet digestibility, respectively. Milk N use efficiency (MNE; i.e., milk N secretion as share of N intake) averaged 24.7 g/100 g N intake (± 5.91), which is greater than observations in temperate, high-input grazing systems but lower than in cows receiving balanced diets in the barn. The MNE and another seven indicators of N utilisation and excretion displayed a wide range of values. The grazing management factors explaining this variation were, thus, identified via backward elimination. The supplementation strategy had the greatest potential for manipulating N utilisation and excretion of dairy cows. Increasing shares of fresh forages (i.e., meadow grass or clover-grass leys) as well as of hay in supplement DMI increased N utilisation (e.g., MNE) and decreased urinary N excretion (e.g., urinary N to creatinine ratio), while increasing shares of concentrates in supplement DMI are related to lower N losses via urine. At the same time, increases in total supplement DMI reduced N utilisation and increased urinary N excretion. Hence, full-time grazing combined with supplementation of fresh forage and hay in the barn is a viable option for low-input, grazing-based dairy operations with moderate levels of N losses.