Recent studies suggest that gut microbiota composition, abundance and diversity can influence many chronic diseases such as type 2 diabetes. Modulating gut microbiota through targeted nutrition can provide beneficial effects leading to the concept of personalized nutrition for health improvement. In this prospective clinical trial, we evaluated the impact of a microbiome-based targeted personalized diet on hyperglycaemic and hyperlipidaemic individuals. Specifically, BugSpeaks®- a microbiome profile test that profiles microbiota using next generation sequencing and provides personalized nutritional recommendation based on the individual microbiota profile was evaluated. The test arm [microbiome-based nutrition] showed a statistically significant decrease in HbA1c level [from 8.30 ± 1.12 to 6.67 ± 0.89, p<0.001] after 90 days. The test arm, also showed a 5% decline in the systolic pressure whereas the control arm showed a 7% increase. Incidentally, a sub-cohort of the test arm of patients with >130mm Hg systolic pressure showed a statistically significant decrease of systolic pressure by 14%. Interestingly, CRP level was also found to drop by 19.5%. Alpha diversity measures showed a significant increase in Shannon diversity measure [p<0.05], after the microbiome-based personalized dietary intervention. The intervention led to a minimum 2-fold [Log2 fold change] increase in beneficial species likePhascolarctobacterium succinatutens, Bifidobacterium angulatum, Levilactobacillus brevis, and a similar decrease in non-beneficial species likeAlistipes finegoldii, Sutterella faecalis. Overall, the study indicated a net positive impact of the microbiota based personalized dietary regime on the gut microbiome and correlated clinical parameters.