Association analyses between longitudinal changes in diet quality scores (DQIs) and cardiometabolic risk remain scarce. Hence, we aimed to investigate how changes in two DQIs are associated with incident type 2 diabetes (T2D), myocardial infarction (MI) and stroke in the EPIC-Potsdam study. Changes in the Mediterranean Pyramid Score (MedPyr) and Healthy Diet Score (HDS) over 7 years from baseline (1994–1998) to follow-up 3 (2001–2005) were investigated in 23,548 middle-aged participants. Adjusted Cox Proportional Hazards Regression models were applied to investigate associations between changes in MedPyr and HDS and chronic disease incidence. More than 60% of the participants increased both DQIs more than 5%. Within a median follow-up time of 5 years 568 cases of T2D, 171 of MI, 189 of stroke were verified. An increased compared to stable MedPyr was associated with lower T2D risk (HR 0.74; 95% CI 0.59–0.92), while a decreased MedPyr was associated with higher stroke risk (HR 1.67; 95% CI 1.02–2.72). A decreased compared to stable HDS was associated with higher stroke risk (HR 1.80; 95% CI 1.02–3.20). The findings contribute further evidence on advantages of changing dietary intake towards a Mediterranean Diet. Although baseline HDS adherence was associated with T2D and stroke risk, longitudinal changes in HDS were only significantly associated with stroke risk.