Start with fresh mushrooms
Select mushrooms that are firm, light, smell fresh and are not bruised, wet, or sticky. The stems of fresh mushrooms should not appear dried out and the gills, if exposed, should be undamaged.
Use them as soon as possible—within a few days of buying them. If you need to store them before use, refrigerate them in their original plastic packaging. If they were purchased loose (or foraged by a trusted mushroom expert), put them in a paper bag and they’ll hold well for a few days. After that, they’ll start to dry out.
Wrapping them in a paper towel and then storing them in an open plastic bag (to prevent condensation from building up) might lengthen their shelf-life another day or so but can also darken the surface of the mushrooms.
When to wipe
Regardless of how you prepare them, if the mushrooms are mostly free of dirt and debris, a brief wiping is enough to get them clean. A lot of cultivated mushrooms are so pristine they hardly need more than a dusting. I’ve never needed to wash maitake, portobello, shiitake, or oyster mushrooms, for example.
Especially if you'll be eating the mushrooms raw (and they are not very dirty), it’s best to simply wipe them clean with a slightly damp towel or a soft brush. Rinsing them with water, on the other hand, can leave the surface of the mushroom slightly slimy—not a texture you’d want in a raw mushroom.
If necessary, clean with water
If mushrooms have dirt that is hard to remove with a towel or small brush, you can give them a rinse. Don’t leave them to soak, just swish them around to release the debris and drain the water. Sometimes it’s necessary to do multiple rinses before the mushrooms are clean.
It’s amazing what will emerge from the little crevices of a morel when you wash it. Small bits of twig, hidden soil, and the not-so-occasional live inhabitant. I know it looks like the mushrooms are soaking here, but I had to pause the rinse for a second to admire the white maggoty thing coming out of the large morel.
Generally, cool water does the job. If you suspect there are things living in the mushrooms, warm water helps draw them out. Some people like to use salted water; I would follow up with a final rinse of unsalted water if using this method.
Dry mushrooms well and use soon thereafter
Blot washed mushrooms with a dry towel and allow air to circulate around them so they can dry further. A wire rack works well.
Trim the stem
Shiitake stems are a little too tough for eating, trim them close to the cap.
Most other mushrooms, including white button, crimini, morels, portobellos, can be trimmed close to the base of the stem.
If you are stuffing the mushrooms, and therefore need to remove the stem entirely, reserve the stem for stock or chop it up and add it to the stuffing.
Removing gills and peeling are optional
It’s not necessary to remove the gills. In the case of portobello mushrooms, the gills can stain other food it comes in contact with. If you don’t want this to happen, scrape the gills out with a spoon.
Mushrooms don’t need to be peeled except for cosmetic purposes.
Trim away damaged spots and split up clusters
Cut off bruised or spoiled spots and other blemishes with a small paring knife.
Mushrooms that grow in large clusters should be broken down by gently splitting them open along the grains of their growth.
Now you're ready to prepare the mushrooms whatever way your recipe or whimsy dictates. Keep in mind that, in general, wild mushrooms should be cooked before eating.