This study explores the effect of different settings on beer fermentation process applying an interval-based version of ASCA on FT-IR data. Three main factors (yeast type, temperature, fermentation time) are included in the experimental design, being high sources of variation in brewing and strictly interdependent; thus, difficult to be studied through a univariate approach. The three-factor full factorial design leads to a spectral multi-set data, with a total of 12 independent fermentations, which is explored combining ASCA and an interval adaptation of ASCA (interval-ASCA or i-ASCA). The ASCA models calculated on two separate regions (2900–2250 cm−1 and 1500–980 cm−1) shows differences for average time levels and the interaction between yeast types and time linked to carbon dioxide, maltose consumption and ethanol production, respectively. To better investigate the punctual influence of the studied factors on the so-called IR fingerprint region, permutation testing of ASCA in variable intervals is investigated. The analysis highlights the significant effect not only of the fermentation in all intervals considered, but also the role of other factors, such as time × yeast, yeast and temperature, in smaller variable regions. The proposed approach demonstrates how interval-ASCA on FT-IR data, isolating the variation in the data according to the experimental design used, allows a rapid and accurate test for parameter control in beer manufacturing