In vivo genome editing offers a long-term therapeutic approach for monogenic diseases by directly modifying genetic sequences. However, its application to non-monogenic, noncommunicable diseases, which are the leading causes of global mortality, remains limited due to the lack of well-defined genetic targets. We developed an in vivo genome-editing approach to introduce a gene encoding the glucagon-like peptide-1 (GLP-1) receptor agonist Exendin-4, modified with a secretion signal peptide. Mice with obesity and pre-diabetic conditions received a single administration of genome editing. Blood Exendin-4 levels, food intake, body weight, and metabolic parameters were monitored over several months. Here we show that in vivo genome editing enables sustained Exendin-4 secretion from liver cells, leading to prolonged elevation of Exendin-4 levels in the bloodstream. Treated mice exhibited reduced food intake, attenuated weight gain, and improved glucose metabolism and insulin sensitivity without detectable adverse effects. This study demonstrates that a single administration of genome editing can achieve sustained therapeutic peptide secretion, providing a potential strategy for treating complex diseases without defined genetic causes. Hirose et al. demonstrate a genome editing-based strategy to treat obesity and pre-diabetes, complex diseases without a defined genetic cause. A single in vivo knock-in of a secretion-engineered Exendin-4 gene into the liver enables sustained peptide release, reducing body weight and improving glucose metabolism in mice. Many diseases, such as diabetes and obesity, are not caused by a single change in a person’s DNA so are difficult to treat with regular gene therapy, a treatment type that modifies DNA. In this study, we used genome editing, a tool that makes precise and lasting changes to DNA. We used it to help the body produce and release a beneficial molecule called Exendin-4, which controls appetite and blood sugar. In mice, just one treatment led to long-term improvements in weight and blood sugar, without noticeable side effects. This study suggests that genome editing could be used to create lasting treatments for complex diseases, potentially reducing the need for frequent medication.