When I get fosters/rescues that come through our house, I disinfect everything with a dilute bleach solution, then a good wash down to get the bleach off for the next time that I use it.  Litter boxes get soaked in bleach water, wicker stuff like hay baskets get dunked in boiling water, cardboard gets tossed and linens go into the wash.  If the linens have a lot of pee on them, I’ll put 1/4 cup of white vinegar in the wash to knock down the smell.  The tarps and the bottom of the dog pen are the hardest to clean, I usually just wipe them down with a dilute bleach solution, then hose them off in the back yard.

I do not use a formula for the bleach, just pour a couple of capfuls into a bucket of hot water and run with it.  Since you are worried about E. cunculi, I do not know if bleach takes them out or not.  I am most concerned with Coccidia, because most of our rescues have been in the wild for a while, and most of them pick it up along the way.

Handwashing with hot water and soap should do the trick.

There are a lot of non-toxic, pet-safe cleaners you can find like Simple Green or George Foreman”s Knock-Out (not kidding)… When I clean out my guinea pig’s crate, I tend to just use a vinegar and water solution. Works well and since I cover it with bedding afterward, the smell doesn’t stay.

i use simple green on the floors if the bunnies miss their box.

As far as general cleaning goes vinegar solution (50/50) works well, but to kill e.cuniculi spores, the only thing that does that is to use a bleach/water solution (10% bleach) and it needs to sit for 2 minutes before wiping. I know that is not practical with carpet, so that would’t work. And as far as I know, there is no way to get spores out of carpet.

Binkybunny, just a thought, what about something like those very hot steam disinfectors in those canisters that you plug in?  Would that kill the spores?  One would think that the heat would kill it too.

Scarlet, sorry for my delay.  I am playing catch-up tonight.  I don’t know f the hot steam disinfectors would do it. Good Question. I’ll have to put it in my "to research" list.

Oh hey no problem! I need to call my vet and schedule a check up for my two and will put that on "my list." LOL My vet just gets this quirky look on his face when he sees me (He knows he’s in for it!) and this list of questions I whip out.  Of course it’s all in good humor and in my defense, I just like to be informed and dang it, I’m going to get my money’s worth out of him!!! LOL He told me he brushes up on his bunny knowledge before I come in because I always ask the "odd but good questions". LOL

I use vinegar. White vinegar diluted. It hits the spot!