Background <p>The risk allele (G) of <i>MTNR1B</i> rs10830963 has been associated with impaired glucose tolerance, increased fasting glucose and type 2 diabetes (T2D). Late evening eating, when endogenous melatonin levels are elevated, is associated with impaired glucose control in <i>MTNR1B</i> risk carriers. Endogenous melatonin levels remain elevated into the morning so may influence glucose response to breakfast.</p> Objective <p>To investigate the interaction of <i>MTNR1B</i> genotype and type of breakfast on postprandial glucose response in a real-world setting.</p> Methods <p>Following an overnight fast, participants consumed either a standard carbohydrate-rich or protein-enriched porridge breakfast. Post-prandial glucose levels were recorded for two hours using a continuous glucose monitor (CGM). One week later, participants repeated the protocol consuming the alternate breakfast. A two-way mixed ANOVA determined the effect of breakfast and genotype on post-prandial glucose levels.</p> Results <p>Fifty-four adults completed the study. Fasting glucose was significantly higher (<i>p</i> = 0.008) in GG (5.53 ± 0.43 mmol/L) compared to CC or CG participants (5.02 ± 0.42 and 5.19 ± 0.52 mmol/L). Post-prandial iAUC was significantly greater following the carbohydrate-rich breakfast compared to the protein-enriched breakfast (<i>p</i> &lt; 0.001). Following the carbohydrate-rich breakfast iAUC was significantly greater in GG participants compared to CC (<i>p</i> = 0.026) and CG participants (<i>p</i> = 0.029). There was no significant difference between genotype groups following the protein-enriched breakfast (<i>p</i> &gt; 0.05).</p> Conclusion <p>The study findings demonstrate, in a relatively young and healthy population, <i>MTNR1B</i> genotype significantly affects markers associated with T2D risk. Personalised genotype-based advice to adjust timing and composition of meals consumed when endogenous melatonin levels are increased may reduce subsequent T2D risk.</p>