Over the years, anthropogenic sources have increasingly affected food quality. One of the most sensitive and nutritional matrices affected by chemical contamination is honey, due to the use of acaricides. Recently, the attention has moved to the presence of phthalates (PAEs) and bisphenol A (BP-A), molecules present in plastic materials used both in the production phase and in the conservation of honey. In this study, an analytical method for the simultaneous determination of PAEs (dimethyl phthalate DMP, diethyl phthalate DEP, diisobutyl phthalate DiBP, dibutyl phthalate DBP, bis(2-ethylhexyl) phthalate DEHP, and di-n-octyl-phthalate DnOP) and BP-A was developed. The extraction technique is the ultrasound-vortex-assisted dispersive liquid–liquid microextraction (UVA-DLLME), using 150 µL of toluene as an extraction solvent, followed by the gas chromatography coupled with ion trap mass spectrometry analysis (GC–IT/MS). The developed method is sensitive, reliable, and reproducible: it shows high correlation coefficients (R > 0.999); limits of detection (LODs) less than 11 ng·g−1; limits of quantification (LOQs) less than 16 ng·g−1; repeatability below 3.6%, except BP-A (11.6%); and accuracy below 4.8%, except BP-A (17.6%). The method was applied to 47 nectar honey samples for evidencing similarities among them. The chemometric approach based on Hierarchical Cluster Analysis and Principal Component Analysis evidenced some similitudes about sample origin as well as marked differences between PAE and BP-A sources.