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Unless you are well stocked at all times you may find yourself lacking in the white vinegar department when it comes time to clean the coffee maker.
I know many people go eons between coffee maker cleanings and when the bug strikes to get this task done you want to take advantage of it but if you only have apple cider vinegar on hand (or baking soda) do your best to hold off until you can get to the store and buy a jug of regular old white vinegar.
Yes, you could clean your coffee maker with the apple cider variety. It has adequate acidic pH levels to get the job done but the tannins will leave behind a taste in your coffee maker than will not rinse off as quickly and easily as you'd like.
Some people complain about the smell of white vinegar in their home but this is easy to dissipate and rinse from your machine. Apple cider vinegar will leave a lingering taste that will make your coffee a bit under-performing for some time.
On a related note you can check out this post for another good way of cleaning your coffee maker when you don't have white vinegar on hand. It takes a lot of lemons though - be forewarned.