Sustainable diets should promote good health for both the planet and the individual. While there is a clear association between lower environmental impact diets and better health outcomes, intervention studies are needed to determine the range of dietary changes and to understand inter-individual differences in response. Individuals having different responses to dietary interventions is underpinned by a variety of genetic, phenotypic and behavioural factors. The aim of this review is to apply the findings from previous literature examining inter-individual variation and phenotypic response to the future of sustainable healthy diets. Despite changing diets or improving diet quality, physiological responses are varied in randomised controlled trials. To better understand response, individuals can be grouped based on shared baseline characteristics or by their shared response to an intervention. Studies grouping individuals by shared characteristics use a metabolic phenotyping or metabotyping approach which demonstrates that some phenotypes are more predisposed to respond to a particular intervention. Tailoring dietary advice to metabolic phenotype shows promise for improving health and diet quality. However, more evidence is needed to understand the complexity that will come with whole dietary change in the context of sustainable healthy diets. We envisage a future where metabolic phenotyping is an integral element for prescribing personalised nutrition advice for sustainable healthy diets.