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How much space should I leave in a carboy used as a secondary fermentor? Volumes never turn out just right to exactly fill a 5 or 6 gallon carboy. Do you just leave some space (2 or 3 quarts) or do you go out of your way to get it full to the neck. My beer stays in the secondary for 6 to 8 weeks before bottling, while it finishes fermenting and gets conditioned etc.