The glucagon-like peptide-1 (GLP-1) receptor (GLP-1R) is the target of blockbuster anti-obesity drugs, including peptides such as semaglutide and tirzepatide. GLP-1R has a complex signaling profile, and the effects of modulating this profile are not completely understood. Therefore, tools to dissect the receptor’s activities are desirable. Here, we report a pair of synthetic peptide agonists, both with sustained signaling capacities compared to GLP-1. Surprisingly, these two close analogues showed markedly distinct abilities to induce intracellular receptor trafficking. Structure-activity relationship studies, cryo-EM analysis, and molecular dynamics simulations shed light on the behavior of GLP-1R in response to the new analogues. Collectively, our results support the hypothesis that peptide dynamics play a key role in signal transduction outcomes.