Q: When you cold condition beer in a keg, does it matter whether it is carbonated or not?
— Carey Lewis

A: I prefer to cold condition after carbonation, because you can aggressively remove yeast by racking the beer from keg to keg without worrying about having enough yeast in the beer at bottling time or having yeast that is too tired to work.

The traditional method of lagering, in which the beer is transferred to the lagering tank with some fermentable sugars and healthy, active yeast, gets the carbonation step knocked out in the first few days. The remaining weeks of lagering allow the yeast to mature the beer flavor (by reducing diacetyl, a buttery flavor) and give the beer sufficient time to become very clear. This is the essence of cold conditioning.

Some brewers cold condition flat beer before bottling to achieve flavor maturation and clarity. This method works, but the carbonation step must be addressed. Many find it is easiest to use bottled carbon dioxide for carbonation of these beers. The yeast load is very low, and they wish to keep the beer very clear without worrying about the slug of yeast at the bottom of the keg or bottle. Others want to have a naturally conditioned beer and find it easiest to add a small dose of vibrant yeast to the beer at bottling time. Both methods work, and they both have their pros and cons. I happen to like the all-in-one nature of the traditional lager process.