Secondary Fermentation is the process of taking your ‘finished’ beer and transferring it to a secondary/conditioning tank, leaving behind any dregs. This is usually done as a conditioning stage to clarify the beer, or you can add other ingredients into the tank to possibly impart a flavor such as coffee, fruit, or more hops. The reason why you cant just leave it in the primary tank, is because once the primary fermentation has slowed and is not producing large amounts of protective carbon dioxide, oxygen will affect the beer, producing those stale, oxidized flavors. If we’re going to let the beer sit after its main fermentation is done, it needs to be away from the spent yeast that accumulates at the bottom of your fermenter. This is because when yeast run out of that sugar to eat they will find other things to munch on such as dead yeast cells. Unfortunately, when the yeast go down this metabolic pathway, they don’t produce the carbon dioxide and ethanol. Instead, through a process known as “autolysis” they produce some off putting flavors, similar to burning rubber.
Longer aging using secondary fermentation will generally smooth out the beer, giving you a more pleasant tasting brew. In the case of lager beers, this type of yeast requires a long, cold secondary fermentation. As the yeast consume the sugars, they leave odds and ends of more complex sugars around, and will eventually turn to them into nourishment. This process can take anywhere from a month or longer since the cold slows down the activity of the yeast.
Ale yeasts, on the other hand, cannot process these more complex sugars and therefore require less time in a secondary fermentation. Once your ale has cleared to your satisfaction in the secondary, it has probably also completed any biological benefits from the secondary fermentation. Secondary fermentations for ales are usually on the order of a week or so, though it won’t hurt the beer to stay in the fermenter longer (but remember that hop flavors and aroma may fade over time). “Big” beers, such as barley wines and imperial stouts, may take a long time to finish fermenting, because there is more sugar to consume, and the yeast is struggling in the presence of the higher alcohol content.
Secondary fermentation can also be done in the bottle. When you add priming sugar and bottle your beer, the yeast go through the same three stages of fermentation as the main batch, including the production of byproducts. If the beer is bottled too early, then that small amount of yeast in the bottle has to do the double task of conditioning the priming byproducts as well as those from the main ferment.