While at the University of Bordeaux, where he became a professor of oenology, Peynaud worked at providing scientific explanations for many problems encountered in the process of winemaking. He convinced the wineries to begin picking of grapes at vineyards up to two weeks later than usual, and to complete the picking as quickly as possible. The practice of also picking underripe or rotten grapes was abandoned, so that the selected fruit arriving at the winery was of the best possible quality.
Peynaud introduced crushing and fermenting fruit in separate batches based on vine age, vineyard location, or any other factor that resulted in fruit of differing qualities in order to control tannin extraction. He then applied the cool fermentations used in Champagne to still white Bordeaux in order to control fermentation temperatures.
Proposing methods that ran counter to many traditions, in the 1950s and 1960s skeptics would use the term "Peynaudization" of Bordeaux, but as his advice clearly produced superior wines, criticism came to an end.
Peynaud considered the control of malolactic fermentation to be one of his most important contributions to winemaking. It was commonly believed that malolactic fermentation was a sickness. He helped the wineries realize that they needed to encourage and control malolactic fermentation. He also stated, "Using only the very best grapes is a new phenomenon," considering this "the crowning achievement of [his] work."