Calcitonin gene-related peptide (CGRP) and adrenomedullin (AM) are peptide hormones and their receptors play a critical role in migraine progression and blood pressure control, respectively. CGRP and AM receptors are structurally related since they are the complex of the calcitonin receptor-like receptor (CLR) with the different types of receptor activity-modifying protein (RAMP); the CLR complex with RAMP1 is the CGRP receptor while the CLR complex with RAMP2 is the AM receptor. The extracellular domain (ECD) of CLR and RAMP provides a binding site for peptide ligands as reported in crystal structures. Several crystal structures of the CGRP and AM receptor ECD used maltose-binding protein (MBP) as a tag protein to facilitate crystallization. Unexpectedly, the recent crystal structures of CGRP receptor ECD showed that the N-terminal MBP tag located in proximity of the bound/mutated peptide ligands. The objective of the current study is to investigate potential chemical interaction between peptide ligands and the MBP tagged to the CGRP receptor ECD. Peptide ligand interaction with purified CGRP receptor ECD was evaluated with fluorescence polarization/anisotropy peptide binding assay with a fluorescent peptide probe. The results of the current study provided evidence that MBP N-terminally tagged to the CGRP receptor ECD formed chemical interaction with mutated peptide ligands. Interestingly, N-glycosylation of the CGRP receptor ECD was predicted to prevent MBP docking to the mutated peptide ligands. The N-glycosylation of CLR ECD N123 was the most critical for inhibiting MBP interaction with the mutated peptide ligands. The MBP tag protein interaction was also dependent on the sequence of the peptide ligands. An endogenous CGRP fragment did not appear to interact with the MBP tag. In contrast to the CGRP receptor, the MBP tag was not involved in peptide ligand binding at AM receptor ECD. Here, I provided evidence that N-glycosylation of the CGRP receptor ECD inhibited the MBP tag protein interaction suggesting an additional role of N-glycosylation in the MBP-tagged CGRP receptor ECD. This study reveals the importance of using a tag protein-free CGRP receptor ECD for the accurate assessment of peptide ligand affinity.