Potassium dihydrogen phosphonate had been allowed as a plant strengthener in organic viticulture in the European Union only until 2013, supporting the control of grapevine downy mildew. Therefore, low or nondetectable levels are a prerequisite for marketing of organic wines and, consequently, validated analytical methods are of major interest. Herein, two methods based on ion chromatography conductivity detection (IC-CD) or ion chromatography inductively coupled plasma mass spectrometry (IC-ICP-MS) for the determination of phosphonic acid (H3PO3) from 14 different plant matrices of Vitis vinifera L., wine, and soil were developed, validated, and compared. Extraction recoveries ranged from 95.1 to 99.3%. Limits of quantification (LOQ) ranged in liquid and solid samples from 3.8 to 16.8 μg/kg and 0.08 to 2.41 mg/kg for ICP-MS detection and from 39.9 to 593.7 μg/kg and 3.51 to 58.7 mg/kg for CD, respectively. Data on a current anonymized selection of 100 conventionally and 30 organically produced wines are briefly presented to demonstrate the suitability of the method.