Novel drug delivery systems targeting native, transplanted, or cancerous beta-cells are of utmost importance. Herein, we present new exendin-4 derivatives with modified unnatural amino acids at strategic positions within the polypeptide sequence. The modified peptides allowed modular orthogonal chemical modifications to attach imaging agents and amphiphilic squalene-PEG groups. The resulting conjugates, SQ-PEG-ExC1-Cy5 and SQ-PEG-ExC40-Cy5 fluorescence probes, display low nanomolar affinity to GLP-1R in fluorescence-based binding assays with EC50 at 1.1 ± 0.2 and 0.8 ± 0.2 nM, respectively. Naturally expressing GLP-1R MIN6 cells and recombinantly transfected CHL-GLP-1R positive cells were specifically targeted by all of the new beta-cell probes in vitro. Specific islet targeting was observed after i.v. injection of SQ-PEG-ExC1-Cy5 with SQ-PEG in normoglycemic mice ex vivo. Semiquantitative biodistribution analysis by epifluorescence indicated prolonged blood half-life (3.8 h) for the amphiphilic Ex conjugate. Liver and pancreas were identified as main biodistribution organs for SQ-PEG-ExC1-Cy5.