The widespread use of agrochemicals raises concerns about environmental impacts, particularly on pollinators, such as bees, which serve as bioindicators of contamination. Developing methods to assess contamination risks in bioindicators supports regulatory frameworks, including EU regulations on the maximum residue limits (MRLs) for pesticides in food and the environment. This study presents the development and validation of two complementary analytical methods (LC-MS/MS and IC-HRMS) for highly polar pesticide (HPP) detection and quantification in bee matrices. Both methods were validated according to document SANTE/11312/2021 v2. LC-MS/MS was validated with a limit of quantification (LOQ) of 0.005 mg/kg for all the analytes. Repeatability at 0.005, 0.010, 0.020, and 0.100 mg/kg showed RSD from 1.6% to 19.7% and recoveries between 70% and 119%. Interlaboratory precision at 0.020 mg/kg across two labs showed RSD from 5.5% to 13.6%, with recoveries between 91% and 103%. The IC-HRMS method achieved LOQs of 0.01 mg/kg (glufosinate, N-acetyl glufosinate, MPPA, glyphosate, N-acetyl glyphosate, N-acetyl AMPA) and 0.1 mg/kg (fosetyl, phosphonic acid, AMPA), with mean recoveries in repeatability conditions from 84% to 114% and RSD from 2% to 14%. Intralaboratory precision showed mean recoveries from 87% to 119%, with RSD values between 10% and 18%. These methods enable accurate monitoring of HPP contamination, supporting risk assessment and sustainable agriculture.