Free fatty acid (FFA) concentrations can be elevated in raw milk due to improper handling and management at the dairy farm, and high concentrations of FFA can lead to off flavors in milk. This study aimed to describe how the herd production system, milking system, feeding and technological factors impact on FFA concentrations in bulk tank milk. FFA concentrations in bulk milk samples from 259 organic and 3326 conventional herds were analyzed by FT-IR during one year. The FFA content was significantly lower in bulk milk from organic than conventional herds. This was most evident during the summer half-year when the organic cows graze pasture. Bulk milk from automatic milking systems (AMS) and tie-stalls contained greater concentrations of FFA than any other milking parlor systems. In AMS, high milking frequency was found to be the most significant contributor to elevated FFA content in milk. Moreover, a strong interaction was found between milking interval and production system (organic vs. conventional). The technical factors, pre-cooling, onset time for cooling after milk inlet, contact between milk and agitation also impacted on the FFA concentration, whereas other technical factors including centrifugal pump type, length and height of pumping line and type of AMS manufacturer were found to be without significant effect on FFA. Feeding variables, based on feeding plans and evaluation, only explained a small part of the variation in bulk milk FFA. Overall, this study demonstrated that AMS compared to other milking system contributes significantly to increased FFA concentration in bulk tank milk, and within AMS high milking frequency contributes to increased FFA concentration.