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The second stage of spontaneous fermentation is dominated by ''Saccharomyces'' species (predominantly ''S. cerevisiae'', ''S. bayanus'', and ''S. pastorianus'', the latter often being present towards the end of this phase). Most of the attenuation is accomplished during this stage, which lasts approximately 3-4 months. In addition to the bulk of the overall ethanol production, this phase also sees the production of higher alcohols and the synthesis of esters, especially isoamyl acetate, as well as glycerol, caprylic acid, and capric acid <ref name="Van Oevelen et al., 1977" /><ref name="Roos_2018" />. It has been reported by some brewers that this stage might begin as early as 3-14 days and corresponds with a drop in pH below that of regular beer, indicating that the first stage for some spontaneous fermentations might be shorter and faster than reported in the other literature <ref>[http://www.spontanmanc.co.uk/?p=66 Zach Taylor of Chorlton Brewing Co. "The Lab Work Begins". Spontanmanc blog. 08/01/2018. Retrieved 08/29/2018.]</ref>. MTF members (both homebrewers and professionals) have observed yeast fermentation activity typically at 3-7 days <ref>[https://www.facebook.com/events/666424196868756/ Various MTF members. Milk the Funk - Collaboration Brew #3: Spontaneous. 05/01/2017. Retrieved 08/29/2018.]</ref><ref>[https://www.facebook.com/groups/MilkTheFunk/permalink/1571139996247542/?comment_id=1571597289535146 Raf Soef, James Howat, Levi Funk. Milk The Funk Facebook thread on how long it takes for yeast to start fermenting in a spontaneous fermentation. 2017.]</ref>. However, these reports are anecdotal based on visual fermentation and microbe analysis was not done in many cases.
The ''[[Saccharomyces]]'' dominated stage of fermentation is followed by prolonged and gradual acid and flavor development accompanied by the final points of attenuation, which lasts anywhere from 2 to 10 months <ref name="Roos_2018" />. 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 often 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" />. When the wort is pre-acidified, the acidification and maturation phases overlap <ref name="Roos_2018" />. Other yeasts such as ''Candida'', ''Cryptococcus'', and ''Torulopsis'' species have also been isolated from mature lambic, although their impact other than possibly being involved in the formation of a pellicle is unknown <ref>[https://onlinelibrary.wiley.com/doi/abs/10.1002/j.2050-0416.1977.tb03825.x MICROBIOLOGICAL ASPECTS OF SPONTANEOUS WORT FERMENTATION IN THE PRODUCTION OF LAMBIC AND GUEUZE. D. Van Oevelen M. Spaepen P. Timmermans H. Verachtert. 1977. DOI: https://doi.org/10.1002/j.2050-0416.1977.tb03825.x.]</ref>. 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" />. Homebrewer Caleb Buck reported data on several batches of homebrewed spontaneously fermented beer and observed a slower drop in gravity for some batches than others over about a 7 month period (see [http://www.archaicpursuit.com/2018/08/2017-coolship-experiment-hopping-rate.html?m=1 this graph for details]).
The acidification phase is also accompanied by the growth of acetic acid bacteria (AAB), which can be undesirable if this growth is excessive since it leads to greater [[Acetic Acid|acetic acid]] production (in high quantities, acetic acid smells and tastes like vinegar and is very harsh on the palate and throat). These microbes include species from the genera of ''Acetobacter'' and ''Gluconobacter''. These microbes are dependent on oxygen in order to metabolize ethanol into acetic acid (with acetaldehyde produced as an intermediate step) and acetoin from lactic acid and are found on the surface of the wort where oxygen is available. The wort/air interface is also where higher concentrations of acetic acid are found due to the AAB being present there rather than deeper within the beer (this is similar to [[Flanders Red Ale]]). It has been shown that the species of AAB found in lambic and American spontaneous ales have adapted to high concentrations of ethanol and acetic acid <ref name="Roos_2018" />. With the flavor threshold of acetic acid in beer being 90 ppm <ref>[https://www.aroxa.com/beer/beer-flavour-standard/acetic-acid Aroxa website. "Acetic Acid". Retrieved 11/19/2018.]</ref>, and levels of acetic acid in Belgian gueuze/lambic being reported in the range of 727-2240 ppm, acetic acid is an important flavor compound in spontaneously fermented beers <ref>[http://beachwoodbbq.com/pdf/BBAIBLTBLENDERY.pdf Ryan Fields. "Brewing Beer in America Inspired By the Belgian Lambic Tradition". 2018.]</ref><ref name="Spitaels et al., 2015" />.
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.