In this work, a new simple method based on a two-step clean-up and gas chromatography-mass spectrometry analysis for the determination of emerging halogenated flame retardants (HFRs), such as dechlorane plus (DP) and brominated phthalates, and polybrominated diphenyl ethers (PBDEs) in different food items was optimized and validated. Several types of food items, i.e. fish (smoked salmon and cod fillet), meat (chicken breast), chicken eggs, cow milk, and extra virgin olive oil, were chosen as representative matrices of the main food categories. After lyophilisation, the food samples were extracted using acetonitrile:toluene (9:1, v/v). As interferences, such as lipids and pigments, were co-extracted, a two-step clean-up (including Florisil and acid silica) was performed to efficiently remove them prior to GC-MS analysis in electron capture negative ionization mode (GC-ECNI/MS). The performance criteria established by the European Commission (2014/118/EU) were achieved with this method for all target analytes, except for the LOQ achieved for BDE-209 (0.1 ng/g wet weight, ww). The trueness ranged between 75 and 125% for most compounds and the matrices analyzed and the repeatability (expressed as RSD%) was <20%, within the set performance criteria. The method was then used for the determination of PBDEs and emerging HFRs in 20 different food items purchased from Antwerp supermarkets, revealing a prevalent contamination with PBDEs (up to 2.02 ng/g ww) and tribromoanisole (up to 6.6 ng/g ww) in the fish/seafood category.