•EEM spectra of cereal flours are measured and modelled by PARAFAC.•PARAFAC provided excitation and emission spectra of dominant flour fluorophores.•PLS-DA using PARAFAC scores is used for classification of flours. This paper presents parallel factor analysis (PARAFAC) of fluorescence of cereal flours. Excitation-emission matrices (EEM’s) of different cereal flours (wheat, corn, rye, rice, oat, spelt, barley and buckwheat) were measured in a front-face configuration over the ultraviolet–visible spectral range. EEM’s showed that flours strongly fluoresce in two spectral regions, where amino acids, tocopherols, pyridoxine and 4-aminobenzoic acid show intense emissions. 4-component PARAFAC was used to model flour fluorescence and to decompose EEM’s into excitation and emission spectra of each component. PARAFAC also provided relative concentrations of these components. The largest differences between flours were found in the concentration levels of the first and third component. Finally, variations in concentrations of PARAFAC modelled components were analysed in relation to the botanical origin of flour samples.