Perfluorinated alkylated compounds (PFAA) have been identified in milk and dairy products at sub ppb levels, however, knowledge on the impact of industrial milk processing on PFAA levels is rare. This study examined industrial milk processing first by analytical screening of products of a cooperating dairy, which varied in kind and number of processing steps. Second, amounts of PFAA in raw milk, cream, skim milk, butter milk, and butter were mass balanced in industrial production. For migration testing, unpacked butter was sampled from the production and exposed to original packaging at 5 °C for 45 days. Screening identified dairy products with high fat contents to bear higher loads of PFAA. The mass balance of butter production revealed a significant impact of phase separation processes on concentrations in fat rich and aqueous phases. Storage of butter in packaging coated with a fluorinated polymer increased butter levels of both PFAA and FTOH.