In organic dairy farming, a goal about improved animal welfare and avoidance of the use of chemicals has introduced restrictions in the use of antimicrobials for treatment of infectious diseases. Mastitis is the major cause of antimicrobial treatments in Danish dairy farming. In order to improve and minimise the use of antimicrobials and the risk of antimicrobial resistance in organic farming, a study based on qualitative research interviews with newly converted organic farmers was carried out. Twenty farmers, 18–26 months after conversion, were interviewed focusing on mastitis treatment patterns and the farmers’ own perception of possible changes in strategies, choices and daily routines linked to mastitis handling. Antimicrobial treatment was the dominant treatment method in these herds, and regarded as the treatment method with best and most well known prognosis concerning a prognosis of cure. Severe symptoms of mastitis and affected general condition of the cow would cause antimicrobial treatment in all herds. Almost all other mastitis treatment choices were based on herd level considerations. Changes due to conversion to organic farming were experienced on the level of land and crop production, and only to a very little extent directly linked to the herd and management choices related to disease prevention and treatment. Veterinary involvement in choices and professional discussions seemed very sparse, and a major challenge for the future development of organic dairy farming must be outlined, in relation to development of explicit treatment strategies based on well-evaluated data analyses, founded on the results from the individual herd.