The market of non-alcoholic and low-alcohol beer has grown continuously thanks to the advocacy for healthy and responsible drinking. Non-alcoholic and low-alcohol products usually possess less higher alcohols and acetates and more aldehyde off-flavors due to the manufacturing processes. The employment of non-conventional yeasts partially mitigates this problem. In this study, we used proteases to optimize the wort amino acid profile for better aroma production during yeast fermentation. The design of experiments was applied to increase the leucine molar fraction, aiming to boost 3-methylbutan-1-ol and 3-methylbutyl acetate (banana-like aromas). This led to an increase from 7% to 11% leucine in wort after protease treatment. The aroma output in the subsequent fermentation, however, was yeast-dependent. An 87% increase of 3-methylbutan-1-ol and a 64% increase of 3-methylbutyl acetate were observed when Saccharomycodes ludwigii was used. When Pichia kluyveri was employed, higher alcohols and esters from valine and isoleucine were increased: 58% more of 2-methylpropyl acetate, 67% more of 2-methylbutan-1-ol, and 24% more of 2-methylbutyl acetate were observed. Conversely, 3-methylbutan-1-ol decreased by 58% and 3-methylbutyl acetate largely remained the same. Apart from these, the amounts of aldehyde intermediates were increased to a varying extent. The impact of such increases in aromas and off-flavors on the perception of low-alcohol beer remains to be evaluated by sensory analysis in future studies.