Alternaria toxins (ATs) are frequently found contaminants in foodstuffs (e.g., alternariol), often reaching high concentrations (e.g., tenuazonic acid). They can spoil a wide variety of food categories (e.g., cereals, vegetables, seeds and drinks) and storage at fridge temperatures does not prevent the growth of Alternaria fungi. Therefore, reliable and validated analytical methods are needed to protect human health and to ensure a transparent and fair trade. This paper describes new technical features that improved a liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the analysis of ATs in tomato, wheat and sunflower seeds. This analytical method should be simple to implement in different laboratories across the EU and thus be an attractive candidate for standardisation. The major element for improvement was the use of isotopically labelled internal standards, only recently commercially available, thereby reducing the sample handling and improving the accuracy of the results. In addition, the sample extraction and the solid-phase extraction (SPE) enrichment/clean-up were fine-tuned, whereas a more suitable analytical column (XSelect HSS T3) with improved selectivity was also employed. Overall, this method shows adequate precision (repeatability < 5.7% RSD; intermediate precision < 7.0% RSD) and trueness (recoveries ranging from 74% to 112%). The limits of quantification in wheat (the most analytically demanding matrix) vary between 0.19 and 1.40 µg/kg. These figures were deemed satisfactory by the European Committee for Standardization (CEN) and have formed the basis for a subsequent interlaboratory validation study. The corresponding standard was published by CEN in 2021.