Is it OK to bottle condition using previously contaminated bottles?

When cleaning suspect bottles is concerned, I personally prefer caustic soda. This is generally considered the nuclear weapon of cleaning and is not usually required for normal cleaning jobs, but when I get bottles that have been standing in someone's driveway for a few months and have stuff growing in it not previously known to Man, accept no substitute. I have also used it for bottles that contained contaminated batches (both with bacterial and wild yeast infections) with good results. The caustic removes molds, yeast residues, tar from cigarette butts, garden refuse, snails and anything else you care to imagine.

* CAUTION * Caustic soda is nasty stuff. Wear gloves and goggles when using it, and always add caustic soda to water, never the other way around.

Make a nice, strong, luke-warm solution of caustic, let the bottles sit in it overnight, rinse with plenty of clean running water the next day. They'll be sqeuaky-clean and ready for use after normal sanitizing.

If the bottles are very contaminated say with sediment sticking and or even if they have been open for a while and have fungal growth inside. You still don’t need to throw away, do the following:

1. Once emptied, wash the bottles with soap and a good bottle brush. Rinse well.

2. Now boil water, add a teaspoon of bleach to the bottle and add the boiling water. Leave for a day.

3. After it’s stood and cool - use a bottle brush again and give it a good scrub with the liquid still inside. Then throw out and rinse.

You should have very clean bottles now, so you can start your normal sanitation (no-rinse) process.

I have used this with very soiled bottles - and I’ve never had a problem or contaminated any new batch.

In your case where it’s contaminated but not open with new growth - you won’t have any problems.

I would actually recommend different chemicals than the others. If you want to be really sure, and have gloves and goggles, I would recommend hot caustic to clean the crud out of the bottles. This is pretty foolproof, but a bit dangerous, so only take this path if you're confident in your safety procedures. The next best bet would be to use a percarbonate cleaner, like napisan, PBW, or similar. This works about as well as caustic, if a little slower, but is much much safer. Make sure you clean the inside AND the outside of the bottles, then after rinsing, inspect against the light. If you see any dirt, wash again (you wash the outside so that you know if there's dirt inside). After washing, sanitise as usual.

Edit: I would also recommend avoiding soap. Any soap residue will kill head, and it's less effective than caustic/PBW anyway. I would personally avoid chlorine based compounds, any poor rinsing will leave unpleasant residues.

Do not only use Starsan. Use water with a bit of bleach added, soak them and clean them, then rinse with a metabisulfite solution.

I did not have any contaminated batches, but in the second half of 2017 I had beers with gushers. I noticed that the chlorine-based cleaning solution I used had gotten old and actually did not contain any chlorine any more. After starting to clean my bottles with a solution of 15 mL chlorine to 6L of water, I got rid of gushing beers in subsequent brews.

It works very well. I had a bottle from West-Vleteren 12 which apparently was not completely clean, containing left over deposits which did not solve easily in water, but the beer inside was drinkable and it did not gush (but it did taste a little bit off).