Pre-diabetes, a condition characterized by elevated blood glucose levels but below diabetes thresholds, is a significant risk factor for the development of type 2 diabetes, as well as other comorbidities including cardiovascular and kidney diseases. Diet plays a critical role in the development of hyperglycaemia and the onset of pre-diabetes. The aim of this study was to assess the impact of a personalized postprandial glucose-targeting diet (PPT), as well as the standard of care Mediterranean diet (MED), on the oral and gut microbiome, metabolites and cytokines in 200 pre-diabetic individuals. This study was a biphasic, randomised, controlled, single-blind dietary intervention. Phase one included a six-month intervention that compared two diets targeting glycaemic control, while phase two included a six-month follow-up period. Participants (n = 225) were randomly assigned in a 1:1 ratio to a PPT (n = 113) or a MED (n = 112). Results showed that participants assigned to the PPT diet had significant changes in 19 gut microbial species, 14 gut and one oral microbial pathway, 86 serum metabolites and four cytokines. Participants assigned to the MED diet showed significant changes in five gut and one oral microbial species, 18 gut microbial pathways, 27 serum metabolites and four cytokines. Authors conclude that dietary interventions can affect the microbiome, cardiometabolic profile and immune response of the host. Thus, diets such as the PPT used in this study, which takes into account microbiome features, could be designed to affect the microbiome and inflict desired metabolic outcomes.