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====Secondary Fermentation====
After primary fermentation the mostly attenuated beer is moved to a secondary fermentation vessel. Often in traditional commercial production secondary fermentation is conducted in wine barrels, however home brewers can accomplish this phase in glass or plastic carboys with low oxygen permeability. A mixed culture of ''Brettanomyces'', ''Lactobacillus'' and ''Pediococcus'' is then introduced to the beer. If barrels are being used then these "bugs" may simply come from the walls of the barrel, originating from a previous batch. Alternatively, the brewer might inoculate the wort with a mixed culture directly, either with a house culture or by introducing the dregs of bottled sour beer. Upon their introduction these new microorganisms begin converting the longer chain sugars left over from the primary fermentation. These sugars are primarily converted into alcohol and lactic acid, increasing the degree of attenuation and lowering the pH of the beer. This also corresponds with a decrease in ''S. cerevisiae'' cell counts, and the release of amino acids and vitamins from yeast autolysis might help fuel lactic acid bacteria and ''Brettanomyces'' <ref name="Hubbe">[https://lookasidewww.fbsbxfacebook.com/filegroups/MilkTheFunk/1407620505932826/Final%20work%202%20-%20Thomas%20H%C3%BCbbe.pdf?token=AWyH17JH23uJ-wby5L7bZBZ-_G9EbxFbtNZhoHdq9nFQXDyOlNW66kYos4cpt_oOzIGzmllGYexkcE6o3bESICERaG8rSM4SruxzJVAaDb7UaoeAfVvLY_7uNezyeiynjnVG1T1zYyf-Zl4f2E6NwyOIX0y9hlh78XXVWFGHZySDEA Effect of mixed cultures on microbiological development in Berliner Weisse (master thesis). Thomas Hübbe. 2016.]</ref>. Other flavor impacting secondary metabolites are also produced, depending on the strains used. In the presence of oxygen, acetic acid is also produced which in low amounts can be complementary, adding to the complexity of the beer.
Some brewers (mostly homebrewers) do not find it necessary to move the mostly attenuated beer into a secondary vessel. Instead, the mixed culture is pitched directly into the primary fermenter. While yeast autolysis is a concern in regular brewing, it is not a cause for concern in mixed fermentations that contain ''Brettanomyces''. Lambic brewers, for example, perform a primary fermentation in barrels, and leave the beer in the barrels during the beer's entire aging process, which is usually 1-3 years <ref>[http://www.lambic.info/Brewing_Lambic#Barrels Lambic.info Wiki. Brewing Lambic. Retrieved 6/8/2015.]</ref>. Yeast autolysis releases trehelose, acids, and other compounds, which are metabolized by ''Brettanomyces'' <ref>[http://www.mbaa.com/districts/michigan/events/Documents/2011_01_14BrettanomycesBrewing.pdf Brettanomyces in Brewing the horse the goat and the barnyard. Chad Yakobson. 1/14/2011.]</ref>. Maintaining a [[Solera]] may be an exception to this (see the [[Solera]] page for details). The advantage of not moving the beer into a secondary vessel is that less overall oxygen is introduced into the beer (oxygen exposure will contribute to more acetic acid and then ethyl acetate production), and may be the best option if the brewer does not have a closed/CO2 system to prevent exposure to oxygen during transferring.
==Finishing Mixed Fermentations==
=== Reusing a Sour Yeast Cake===
Reusing a sour yeast cake can often provide great results. Brewers have reported success re-pitching on very old yeast cakes (2+ years) without getting off flavors from yeast autolysis. After several months, ''[[Saccharomyces]]'' tends to die off due to the low pH in a sour beer. The bacteria and [[Brettanomyces]] tend to survive the lower pH, and their cell counts can be high in even an old yeast cake (interesting, ''Brettanomyces'' remains more viable over time if it was co-fermented with ''S. cerevisiae'' than if it was fermented by itself; i.e. [[100%25_Brettanomyces_Fermentation|100% ''Brettanomyces'' beers]] <ref name="Hubbe">[https://lookaside.fbsbx.com/file/Final%20work%202%20-%20Thomas%20H%C3%BCbbe.pdf?token=AWyH17JH23uJ-wby5L7bZBZ-_G9EbxFbtNZhoHdq9nFQXDyOlNW66kYos4cpt_oOzIGzmllGYexkcE6o3bESICERaG8rSM4SruxzJVAaDb7UaoeAfVvLY_7uNezyeiynjnVG1T1zYyf-Zl4f2E6NwyOIX0y9hlh78XXVWFGHZySDEA Effect of mixed cultures on microbiological development in Berliner Weisse (master thesis). Thomas Hübbe. 2016.]</ref>). By pitching new wort on an old sour yeast cake, these microbes (particularly the [[Lactobacillus]]) have access to the simple sugars in the wort <ref>[http://www.themadfermentationist.com/2009/11/brewing-sour-beer-at-home.html Tonsmeire, Michael. The Mad Fermentationist. Brewing Sour Beer at Home. Last paragraph in the "Inoculation" section. Retrieved 2/19/2015.]</ref>. In general, washing the yeast cake is not necessary.
Some brewers will harvest a certain amount of trub from their fermenters (500mL for example), and use only this amount to inoculate a new batch of beer. This will allow the brewer to control the amount of dead trub material that goes into the new beer. Michael Tonsmeire often advises that the brewer also pitch a fresh culture of Saccharomyces <ref>[http://www.themadfermentationist.com/2009/11/brewing-sour-beer-at-home.html Tonsmeire, Michael. The Mad Fermentationist. Brewing Sour Beer at Home. Comments section. Retrieved 2/19/2015.]</ref>.