There is no risk IF you used an approved salsa recipe. And the separation is normal. It also happens even if you mill them hot, just not as much.

The contents will settle and remix in time. Or before you remove the bands to store the jars you can even carefully invert the jars to remix after they are well cooled.

Dave

Thanks Dave!
The salsa recipe I used is approved for canning BUT in its chunky form. I decided to mill a batch because sometimes I like my salsa to be smooth. When it's canned in chunky form, I don't notice any separation.

Glad to hear that I can go ahead and store the milled salsa for later use (or else I was going to be eating a lot of salsa the next few weeks!)

approved for canning BUT in its chunky form. I decided to mill a batch

That changes the density so the processing time on the recipe wouldn't be sufficient. It is the same issue that arises with any low-acid vegetable or mixed vegetables - chunked is ok but pureed isn't approved because of the density and heat penetration issues it creates.

Freeze the milled salsa.

Dave

I agree with Dave 100%! If you changed the way the recipe was prepared, it isn't the same recipe. Testing was done "as written".

There are recipes out there that include tomato sauce or paste for a smoother/thicker salsa that are tested. Annie's Salsa is one, Oregon State Extension also has one (very similiar). These yield a less watery product and have been tested!

When did you can it? Your original post just said "recently". If it's been several days, you may actually need to throw it out! It's underprocessed and could pose significant risk....is it worth it?

Deanna