During the transition from Late Antiquity to the Middle Ages, the Roman Empire dissolved in the West and medieval empires were founded. There has been much discussion about the role that migration played in this transition. This is especially true for the formation of the Baiuvariian tribe and the founding of this tribal dukedom, which took place from the 5th to the 6th century in what is now Southern Bavaria (Germany). In this study, we aimed to determine the extent of immigration during the beginning of this transformation and to shed further light on its character. To achieve this goal, we analyzed stable isotope values of strontium, carbon, and nitrogen from the teeth and bones of over 150 human remains from Southern Germany, dating from around 500 AD. This group of individuals included women with cranial modifications (ACD) which can be found sporadically in the burial grounds of this period. Our results showed an above-average migration rate for both men and women in the second half of the 5th century. They also indicate that a foreign background may also be assumed for the women with ACD. The demonstrably different origins of the immigrants from isotopically diverse regions, and the identification of local differences in detectable migration rate, as well as indication for different timing of residential changes, highlight the complexity of immigration processes and the need for more studies at the regional level.