Spectral resolution (R) and number of repeated scans (S) have a significant effect on the S/N ratio of Fourier transform-near infrared (FT-NIR) spectra, but the optimal values of these two parameters have to be determined empirically for a specific problem, considering separately both the nature of the analysed matrix and the specific instrumental setup. To achieve this aim, the instrumental noise of replicated FT-NIR spectra of wheat samples was modelled as a function of R and S by means of the Doehlert design. The noise amounts in correspondence to different experimental conditions were estimated by analysing the variance signals derived from replicate measurements with two different signal processing tools, Savitzky-Golay (SG) filtering and fast wavelet transform (FWT), in order to separate the "pure" instrumental noise from other variability sources, which are essentially connected to sample inhomogeneity. Results confirmed that R and S values leading to minimum instrumental noise can vary considerably depending on the type of analysed food matrix and on the different instrumental setups, and helped in the selection of the optimal measuring conditions for the subsequent acquisition of a wide spectral dataset.