Establishing causality in nutrition research is challenging. While randomised controlled trials (RCTs) provide robust evidence, long-term dietary intervention studies with disease endpoints are often impractical. Short-term RCTs can instead identify intermediate traits that may lie on the causal pathway between diet and disease. Mendelian randomisation (MR) is an epidemiological approach that uses genetic variants as proxies for modifiable exposures to estimate the effects of lifelong differences in exposure on disease risk. However, the utility of MR is limited for complex dietary patterns because genetic variants typically reflect biological mechanisms rather than specific diets. We propose a two-step framework integrating dietary RCTs with MR to infer potential lifetime effects of dietary interventions. First, RCT data identify molecular traits altered by an intervention. Second, MR evaluates whether these traits are associated with long-term disease risk. We demonstrate this framework using the Diabetes Remission Clinical Trial (DiRECT), which measured circulating proteins and diabetes remission. Using protein data alone, 216 of 4,601 proteins changed following the intervention (step 1), and 10 were associated with diabetes risk using MR (step 2). We then compared these MR estimates with observed protein-remission associations from DiRECT. The broad agreement between the two (r{approx}-0.645, R2=0.416) supports this framework as a useful approach for estimating long-term effects of dietary interventions.