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Can I store less then 5 gallons in a keg topping it off with CO2? I want to brew and have beer made, but I use 2 1/2 gallon kegs because my frig is small. I picked up a nice clean 5 gallon keg, and planned to store beer in it awaiting an empty 2 1/2 gallon keg.

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There are a few issues with storing beer in any half full container. All of these issues are manageable.

The first issue is oxygenation, but if you flush the keg with CO2 it will be fine while it is in the keg. Storing the keg at room temperature will allow a little bit of additional fermentation and you will wind up with a thicker layer of dead yeast on the bottom. I always have at least some dead yeast on the bottom, but when I store at room temperature the layer is thicker.

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If you adequately purge the keg with CO2 (I like to use the out dip tube side) before putting the beer in you'll be in good shape with any fill level you need to use.

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    I also used this technique recently with 3 gallons of beer in a 5 gal keg and it worked quite well. Like @brewchez said, it is good to start by purging the keg of oxygen before even filling. You can achieve this most effectively by using your diptube in the IN (gas) line to fill CO2 from the bottom up. Don't forget to put the diptube back in the OUT line before you fill and purge. Cheers. – Taliesin Sep 28 '16 at 21:16
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Yes, that is totally fine so long as you blanket it with CO2.

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You definitely can and I do all the time. I still like to bottle parts of my batch so it's easier to being places. Just make sure you purge the keg first and after. Just think of it like starting out with a full keg and drinking half of it.

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