Plant-based product replacements are rising in popularity, however, long-term health implications remain poorly understood, and available methods of assessment hamper population-level determination of nutritional impacts. We examine anonymised loyalty-card shopping records from Co-op Food, UK, to identify dietary transitions over time. We focus on 10,626 frequent customers who directly replaced milk with alternative milks. We then use product nutritional information to estimate weekly nutrient intake before and after the transition. 83% who converted to alternative milk saw a fall in iodine (44%), calcium (30%) and vitamin B12 (39%) consumption with 57% reducing iodine purchase of more than 50%. The decline is even higher for those switching dairy and meat products. Our findings suggest that dietary transitions - such as replacing milk with alternative milks - could lead to nutritional deficiencies, notably iodine, which if not addressed may represent a significant public health concern, particularly in countries which do not mandate salt iodisation.