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Are you using priming sugar or filling from a keg? If priming does that work? I think the yeast need that little oxygen in the headspace to ferment the priming sugar and produce co2. You could be doing more harm than good by purging the headspace in the bottles.
I'm bottling from a bottling bucket, priming and bottle conditioning as usual. I can guarantee you the headspace purging has absolutely no ill effects on carbonation. As said above I usually get fully carbed beer in less than a week, though I'll wait at least 3 to really start drinking it. But after a week I can already put the bottles in the cellar or fridge, cause carbing is over.
I think at that stage the yeast does really not need that oxygen to do it's job. There is still plenty of yeast in suspension,it does not need to multiply further, only to ferment that little amount of priming sugar.