When implementing the transition from regular milk production to the dry period, drying off is mostly conducted simply by abrupt cessation of milking. Efforts to reduce milk synthesis before cessation of milking aim to reduce stress in cows as well as to lower the risk of mastitis. A previous study demonstrated that incomplete milking during the last ten days of lactation gradually reduced the milk yield of healthy, high-yielding cows. However, a reduction period of ten days might be too long for cows with lower yields. Therefore, a follow-up study was conducted on an organic dairy research farm with a lower average milk yield. We investigated whether automated incomplete milking can reduce milk synthesis within one week without impairing the health status of udder quarters infected with minor pathogens. Before drying off, 15 German-Holstein cows with 58 lactating quarters, 21 of which were infected with minor pathogens (coagulase-negative Staphylococci (CNS) and Corynebacterium bovis), were milked twice daily using the software module AutoDry (GEA Farm Technologies) with the 5%-step-down-per-day-program. The level of udder emptying was gradually reduced over 8–10 milkings beginning at a mean milk yield of 17.2 ± 4.4 kg d−1. During the last three milkings before drying off, milking clusters were automatically removed when a milk flow rate of 0.3 kg min−1 was reached. Quarter fore-milk samples were collected at two time points (14 d before and at the date of the last milking, ie drying off) and were analysed for mastitis pathogens and somatic cell count. The gradual reduced emptying of the udder induced a clear decline in milk yield by 0.8 ± 0.3 kg d−1. Within the reduction period, the somatic cell count of quarter foremilk did not change regardless of the infection status. Furthermore, no cow suffered from clinical mastitis. Thus, a reduction in milk synthesis could be achieved within less than one week before drying off without any impairment in udder health of cows, even when infected with minor mastitis pathogens.