Dear Mr. Wizard,
If you are reusing yeast for another beer, should you take it from the first or second fermenter?
Mr. Wizard responds:
I always harvest and re-use our yeast (like other commercial brewers) and the accepted rule is that yeast should be cropped as soon as possible when its viability and vitality are at their peak. Some ale brewers continue to crop yeast from the tops of an open fermenter and this is done towards the end of peak fermentation before the cap begins to fall into the beer . . . although in the case of some top fermenting strains the thick kraüsen never really falls.
Most brewers these days harvest yeast from the bottom of conical fermenters and one must wait until the yeast is on the bottom and can be taken. Our ale flocculates pretty well and we can harvest yeast about 3–4 days after primary fermentation is complete. The longer you wait to harvest and reuse your yeast, the greater the chance of having sluggish, not-so-healthy yeast in your next batch. I would suggest not reusing yeast that has been sitting on the bottom of a carboy for any longer than two weeks.