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The second stage of spontaneous fermentation is dominated by ''Saccharomyces sp.'' (predominantly ''S. cerevisiae'' and ''S. bayanus''). Most of the attenuation is accomplished during this stage, which lasts approximately 3-4 months <ref name="Van Oevelen et al., 1977" />.
The ''Saccharomyces'' dominated stage of fermentation is followed by prolonged and gradual acid and flavor development accompanied by the final points of attenuation. In some descriptions this is split into an "acidification phase" which is dominated by lactic acid bacteria (LAB), primarily ''Pediococcus'', and a "maturation phase" driven by ''Brettanomyces'' <ref name="Van Oevelen et al., 1977" />. Other sources describe these as one extended maturation phase with acidification from ''Pediococcus'' and ''Brettanomyces'' growth occurring simultaneously (note that many scientific publications use the nomenclature ''Dekkera'' rather than ''Brettanomyces'') <ref name="Spitaels et al., 2015" /> <ref name="Bokulic et al., 2012" /> <ref name="Spitaels et al., 2014" />. Note that many scientific publications use the terminology ''Dekkera'' rather than ''Brettanomyces''. As many of the flavor and aroma characteristics that we associate with spontaneously fermented beer are produced during this slow maturation/acidification phase, allowing sufficient aging time is important when producing spontaneously fermented beers <ref name="Van Oevelen et al., 1976" /> <ref name="Spaepen et al., 1978" />.
During the extended maturation phase, a beer may become "sick" or "ropey", though not all producers get this <ref name="Spontaneous Sour Hour" /> (~1:10 min in) <ref name="Vinnie sour beer talk">[http://www.thebrewingnetwork.com/post1863/ Recording of Vinnie's talk at NHC]</ref> (~1:44 in) <ref name="Vinnie on the Session Jan 2010"/> (~3:44 in). This is the result of exopolysaccharides, which some ''Pediococcus'' strains are known to produce. These exopolysaccharides can be broken down by other microbes present in the beer relieving the beer of its "sickness" (this exopolysaccharide breakdown is generally attributed to ''Brettanomyces''). A beer may also become "sick" in the bottle during bottle conditioning. This is likely due to enhanced ''Pediococcus'' activity from additional fermentable sugar, in the form of simple sugars or beer which has not completely attenuated yet <ref name="Vinnie sour beer talk">[http://www.thebrewingnetwork.com/post1863/ Recording of Vinnie's talk at NHC]</ref> (~1:47 in). A beer which is sick in the bottle will generally clear through the same process as a younger aging beer when given appropriate time. See the [[Pediococcus#.22Ropy.22_or_.22Sick.22_Beer|Pediococcus]] page for more information.