Achieving a sustainable and healthy diet requires increased replacement of red meat with more sustainable foods. There is a call for novel methodologies to assess the potential of different interventions and policies in enhancing the transition from the current to more sustainable choices. We aimed to characterize consumer clusters with similar preferences in protein sources, to compare the purchase prices of these foods, and to identify ongoing transitions from one protein source to another. Grocery purchase data with individual attributes on 29,437 consenting loyalty card holders were analyzed over 2.3 year period. We designed a sequence analysis to group participants to clusters with similar purchase preferences over the follow-up period and to estimate transition probabilities between preferences. We studied the determinants of prevalent purchase profiles by ordinal logistic models. We identified six participant profiles with similar preferences in four protein sources: red meat, poultry, fish, and plant-based foods. Red meat dominated the purchase preferences and showed the highest persistence over time. The majority (70%) of the participants demonstrated somewhat mixed purchase profiles. A step-by-step transition from red meat towards plant-based food preference seems most likely via poultry and fish. Overall, low income was not a barrier to a more sustainable purchase profile, while price may deter the purchase of fish. The most important resources in choosing more sustainable profiles were education and stage of family life. Societal incentives for sustainable food choices seem most crucial at transition stages of life course and for the less educated. Here, we also demonstrate that grocery purchase data offer a valuable tool for monitoring the progressive transition towards a healthy and sustainable food system.