The conditioning process is a function of the yeast. The vigorous, primary stage is over, the majority of the wort sugars have been converted to alcohol, and a lot of the yeast are going dormant; but there is still yeast activity. During the earlier phases, many different compounds were produced by the yeast in addition to ethanol and CO2, e.g., acetaldehyde, esters, amino acids, ketones- diacetyl, pentanedione, dimethyl sulfide, etc. Once the easy food is gone, the yeast start re-processing these by-products. Diacetyl and pentanedione are two ketones that have buttery and honey-like flavors. These compounds are considered flaws when present in large amounts and can cause flavor stability problems during storage. Acetaldehyde is an aldehyde that has a pronounced green apple smell and taste. It is an intermediate compound in the production of ethanol. The yeast reduce these compounds during the later stages of fermentation.
The yeast also produce an array of fusel alcohols during primary fermentation in addition to ethanol. Fusels are higher molecular weight alcohols that often give harsh solvent-like tastes to beer. During secondary fermentation, the yeast convert these alcohols to more pleasant tasting fruity esters. Warmer temperatures encourage ester production.
Towards the end of secondary fermentation, the suspended yeast flocculates (settles out) and the beer clears. High molecular weight proteins also settle out during this stage. Tannin/phenol compounds will bind with the proteins and also settle out, greatly smoothing the taste of the beer. This process can be helped by chilling the beer, very similar to the lagering process. In the case of ales, this process is referred to as Cold Conditioning, and is a popular practice at most brewpubs and microbreweries. Cold conditioning for a week clears the beer with or without the use of finings. Fining agents, such as isinglass (fish bladders), Polyclar (plastic dust), and gelatin, are added to the fermentor to help speed the flocculation process and promote the settling of haze forming proteins and tannins. While much of the emphasis on using finings is to combat aesthetic chill haze, the real benefit of dropping those compounds is to improve the taste and stability of the beer.