When in trade or storage casks, beer began a slow secondary fermentation. Maltodextrins were gradually broken down and consumed through the hydrolic action of the yeast, helped by the diastatic enzymes in the dry hops. The fermentable material created in this way was enough to keep the beer saturated with CO2, which helped protect it from bacterial attack. Some of the CO2 combined with water to form carbonic acid. During long storage, esters were formed, which contributed to the character of aged beers.
Standard pitching yeast, a type of Saccharomyces cervesiae, was not capable of performing this type of secondary fermentation. Brettanomyces was the yeast responsible. This gave beers that were matured for long periods the typical "aged taste". Until 1903, when N. H. Clausen isolated Brettanomyces at the Carlsberg laboratory in Copenhagen, the process had been a mystery. Brettanomyces was either a component in a multi-strain yeast, which only really became active during secondary fermentation, or was picked up from wooden equipment. Its discovery explained why single-strain pitching yeasts often struggled to successfully carry out secondary fermentation.
Aged beers were going out of fashion and beers were rarely stored more than a few weeks before shipping. The age of tun rooms, filled with Porter maturing for 12 months or more, had passed. The London breweries had dismantled their massive vats and converted their tun rooms to other uses.
Many beers were not left to mature in the brewery at all, but shipped immediately after racking. In this case any secondary fermentation took place in the pub cellar. Today most cask-conditioned beer is handled this way. Sykes & Ling did not think this a true secondary fermentation, but an extension of primary fermentation, as only the easily-fermentable sugars were being consumed. They only considered the slow fermentation of maltodextrins over a period of many months as a true secondary fermentation.
Different breweries might have very different methods of storing casks for ageing.
"The methods of storing beer in different parts of the United Kingdom vary considerably. In Burton the beer is run into the trade casks, and these are often stacked in the open during the winter months, and only placed under cover as the season advances. In other localities the trade casks full of stock beer are stored in underground cellars, where a very uniform temperature is maintained. Of these two plans, the former answers well if the beer is sound and good enough to stand it, but if there is any doubt on this point the latter plan must of course be adopted. Then again, black beers and old ales are frequently stored in vats, and vatting greatly improves the quality of these varieties of malt liquor."
The rough treatment given to some beers actually seemed to make them more robust:
"The fact is, that by coddling beers, while you certainly preserve them from disease, you are sure at the same time to render them tender, and susceptible to every change of temperature. Burton beers, in former days, were exposed by day to the heat, and by night to the frost, and, by this treatment, they became so hardy that they retained their condition and brilliancy under the most adverse circumstances."