Saccharomyces cerevisiae is commonly used for the production of alcoholic beverages, including cider. In this study, we examined indigenous S. cerevisiae and S. uvarum strains, both species commonly found in cider from Hardanger (Norway), for their strain-specific abilities to produce volatile and non-volatile compounds. Small-scale fermentation of apple juice with 20 Saccharomyces strains was performed to evaluate their aroma-producing potential as a function of amino acids (AAs) and other physicochemical parameters under the same experimental conditions. After fermentation, sugars, organic acids, AAs, and biogenic amines (BAs) were quantified using the HPLC–UV/RI system. A new analytical method was developed for the simultaneous determination of nineteen AAs and four BAs in a single run using HPLC–UV with prior sample derivatization. Volatile compounds were determined using HS-SPME-GC-MS. Based on 54 parameters and after the removal of outliers, the nineteen strains were classified into four groups. In addition, we used PLS regression to establish a relationship between aroma compounds and predictor variables (AAs, BAs, organic acids, sugars, hydrogen sulfide (H₂S) production, CO₂ release) of all 19 strains tested. The results of the VIP show that the main predictor variables affecting the aroma compounds produced by the selected yeasts are 16, belonging mainly to AAs.