Background: Although glyphosate is widely used in agriculture, information on its residue level in soils remains scarce partly because of the difficulty in its analysis. Objective: Develop and validate a method to directly analyze glyphosate and its metabolite aminomethylphosphonic acid (AMPA) in soil. Method: Soils were extracted with 0.6 M KOH solution, and coextracted interferences were removed using a mixed-mode Bond Elut Plexa PAX®. The extracts were analyzed by LC-tandem MS fitted with a Hypercarb column and isotope-labeled (13C,15N) glyphosate and AMPA were used as internal standards. Results: LOQs were 0.05 mg/kg for both glyphosate and AMPA in soils. Correlation coefficients were ≥0.99, residuals were below 20%, and calibrations were linear in the range 0.02–1.0 μg/mL. The method was validated on five contrasting soils (Vertosol, Calcarosol, Chromosol, Sodosol, and Tenosol) commonly used for grain production in Australia. The recoveries for glyphosate and AMPA in the soils were 96–121 and 91–118%, respectively, with RSD in the range of 3–16%. Conclusions: This paper presents using the validated method in analysis glyphosate and AMPA in soils collected from crop production paddocks in Australia. The survey data showed that glyphosate and AMPA were detected in all collected soils, with concentrations ranging between 0.05 and 1.2 mg/kg. Highlights: The study demonstrates that the mixed-mode solid-phase extraction is effective in removing interferences and validates the use of Hypercarb as an alternative stationary phase for glyphosate and AMPA analysis from soils.