Honey, a component of the European diet, faces contamination challenges that impact both consumer and bee health. Glyphosate and glufosinate-based herbicides are widely used in both agriculture and domestic settings, posing potential threats to humans and bees. This study addresses the need for robust analytical methods to detect glyphosate, glufosinate, and their metabolites in honey, considering the complexities of the matrices. Advanced techniques, such as Liquid Chromatography-Mass Spectrometry (LC-MS/MS) and Ion Chromatography-High-Resolution Mass Spectrometry (IC-HRMS) were employed for method validation and monitoring across 97 honey samples. The extraction procedure was optimized, and the validation procedure followed EU Regulation 808/2021 and SANTE 11312/2021 guidelines. LC-MS/MS and IC-HRMS demonstrated comparability and high sensitivity, with RSDr and RSDR values falling within the range of 3%–18% and 6%–22%, respectively, for all analytes considered except for AMPA. AMPA showed CV% values > 25% at the concentration of 5 and 10 ng/g in LC–MS/MS. For IC-HRMS RSDr and RSDR values for all analytes fall within the 3%–14% and 4%–14% range, respectively. Glyphosate was quantified in 12% of the samples, with one sample exceeding Maximum Residue Level (MRL). Glufosinate and its metabolites were not detected in any of the samples.