Functional food has been highly demanded lately because of its benefits in counteracting diseases. Fucoidan and agave fructan are ingredients that enhance the growth of beneficial bacteria in the gut (prebiotics). This mixture has great potential to develop innovative products but it has never been explored before. Because of fucoidan is more expensive than agave fructan, the innovative proposed mixture is vulnerable to adulteration. This research was aimed to assess the accuracy of Fourier transform infrared spectroscopy with attenuated total reflectance (ATR–FTIR) coupled with chemometrics to identify and predict concentration of both polysaccharides in powder mixtures (0–100%). Absorption bands at 1240–1255 and 836–840 cm⁻¹ were attributed to fucoidan and a strong peak at ~ 936 cm⁻¹ confirmed the fructan presence. Peak areas were best fitted into linear models ( ≥ 0.92, RMSE ≤ 3.54%). This achievement may be useful to certificate ingredients contained in fucoidan–fructan mixtures, preventing adulteration.