It is estimated that more than 20% of processed apples and grapes are discarded as waste, which is dominated by pomace rich in malic acid that could be converted to high-value organic acids or other chemicals. A total of 98 yeast strains isolated from apple, grape, and plum wastes were evaluated for their ability to degrade malic acid relative to known yeast strains. Most (94%) of the new isolates degraded malic acid efficiently (> 50%) in the presence and absence of exogenous glucose, whereas only 14% of the known strains could do so, thus confirming the value of exploring (and exploiting) natural biodiversity. The best candidates were evaluated in synthetic media for their ability to convert malic acid to other valuable products under aerobic and oxygen-limited conditions, with two strains that produced ethanol and acetic acid as potential biorefinery products during aerobic cultivations and oxygen-limited fermentations on sterilized apple and grape pomace. Noteworthy was the identification of a Saccharomyces cerevisiae strain that is more efficient in degrading malic acid than other members of the species. This natural strain could be of value in the wine-making industry that often requires pH corrections due to excess malic acid.