Glucagon-like peptide-1 receptor (GLP-1R) agonists are a highly effective therapy class for type 2 diabetes (T2D) and obesity, yet there are variable patient responses. Variation in the human Glp1r gene leading to altered receptor structure, signal transduction, and function might be directly linked to therapeutic responses in patients. A naturally occurring, low-frequency, gain-of-function missense variant, rs10305492 G>A (A316T), protects against T2D and cardiovascular disease. Here we employ CRISPR/Cas9 technology to generate a humanised knock-in mouse model bearing the homozygous Glp1r A316T substitution. Human Glp1r A316T/A316T mice displayed lower fasting blood glucose levels and improved glucose tolerance, as well as increased plasma insulin levels and insulin secretion responses, even under metabolic stress. They also exhibited alterations in islet cytoarchitecture and β-cell identity indicative of compensatory mechanisms under a high-fat, high-sucrose (HFHS) diet challenge. Across all models investigated, the human Glp1r A316T variant exhibited characteristics of constitutive activation but blunted incretin-induced responses. Our results are further supported by cryo-EM analysis and molecular dynamics (MD) simulations of the GLP-1R A316T structure, demonstrating that the A316T Glp1r variant governs basal receptor activity and pharmacological responses to GLP-1R-targeting anti-diabetic therapies, highlighting the importance of the precise molecular characterisation of human Glp1r variants to predict individual therapy responses.