Phycotoxin accumulation in seafood can cause human intoxication and significant economic losses in seafood-producing areas. To protect consumer safety, maximum permitted levels in bivalve molluscs have been set, with appropriate analytical methods for their determination and quantification. The reference method for lipophilic phycotoxins, commonly referred to as lipophilic toxins, is liquid chromatography tandem mass spectrometry (LCMS/MS method), where coeluting components from the matrix can affect the efficiency of ionisation, resulting in erroneous quantification. In this study, the matrix effect was evaluated using the slope ratio analysis method, which involves comparing the slopes of the calibration curves in the matrix with those in pure solvent. The extent of the matrix effect was investigated in mussels, oysters, queen scallops and ascidians. The study covered all phycotoxins under Regulation EU 853/2004 for which certified standards are commercially available, including unregulated pectenotoxin 2. The results indicated that all lipophilic toxins were susceptible to this effect when LC-MS/MS was used for their determination. Significant ion suppression was evident for most analytes in all matrices, except for okadaic acid and dinophysistoxin 2 in bivalves, where significant ion enhancement was demonstrated, and dinophysistoxin 1 in oyster and scallop extract where no significant effect on ionisation was observed. Further analysis revealed no significant differences between the slope of mussel matrix-matched calibration and that of other bivalve matrices. Given this minor difference, the mussel matrix-matched calibration curve could be applied to minimise the matrix effect and to quantify phycotoxins in bivalve matrices analysed here, with the exception of the okadaic acid group in ascidians, which requires matrix-matched calibration prepared with the blank extract of these mentioned species. Given the risks phycotoxins pose to human health, ongoing analytical method development is necessary in this field to properly control food safety and ensure consumer health.