During the secondary fermentation and aging process, which takes three to six months, the fermentation continues very slowly. The wine is kept under an airlock to protect the wine from oxidation. Proteins from the grape are broken down and the remaining yeast cells and other fine particles from the grapes are allowed to settle. Potassium bitartrate will also precipitate, a process which can be enhanced by cold stabilization to prevent the appearance of (harmless) tartrate crystals after bottling. The result of these processes is that the originally cloudy wine becomes clear. The wine can be racked during this process to remove the lees.

The secondary fermentation usually takes place in large stainless steel vessels with a volume of several cubic meters, oak barrels or glass demijohns (also referred to as carboys), depending on the goals of the winemakers. Unoaked wine is fermented in a barrel made of stainless steel or other material having no influence in the final taste of the wine. Depending on the desired taste, it could be fermented mainly in stainless steel to be briefly put in oak, or have the complete fermentation done in stainless steel. Oak could be added as chips used with a non-wooden barrel instead of a fully wooden barrel. This process is mainly used in cheaper wine.

Amateur winemakers often use glass carboys in the production of their wine; these vessels (sometimes called demijohns) have a capacity of 4.5–54 litres (0.99–11.88 imp gal; 1.2–14.3 US gal). The kind of vessel used depends on the amount of wine that is being made, the grapes being used, and the intentions of the winemaker.