Heat a large pot, saucepan, or Dutch oven over medium heat. Once hot, add oil, butter, or water and the sliced onions (they should be ~1/4 inch thick so the soup has nice texture). Stir and cover.
Cook the onions over medium heat for 3-4 minutes or until they start to very slightly brown. Then turn heat to low and cook for a total of ~30-40 minutes, opening the lid and stirring every 5 minutes. The name of the game with caramelizing onions is to cook slow and low. NOTE: If cooking without oil, be sure to cover the pot with lid after stirring — this helps them cook more evenly. And add 1 Tbsp water more at a time as needed to prevent sticking/ burning.
How long you cook your onions depends on how deeply you want them caramelized. We found 30 minutes to produce a light golden brown color and sweet flavor, and 35-40 minutes to yield a deeper brown color and richer caramelized flavor. Be careful not to burn by keeping heat on low and adding a bit of water or broth as needed to prevent sticking.
Add a healthy pinch of salt and pepper while sautéing, plus more to taste later as you season the soup.
When your onions are close to being caramelized, add minced garlic and mushrooms and sauté for 2-3 minutes more. Then add arrowroot starch (optional, for slight thickness) and stir to fully combine (it should absorb fully into the onion mixture). Use a wooden spoon to disperse any clumps.
Add bay leaf, dried or fresh thyme, vegetable broth, and coconut aminos (reserve the miso for later).
Cover and simmer soup for about 20 minutes to develop and meld the flavors. Then simmer uncovered for another 5-10 minutes so it thickens slightly (the flavors will intensify even more). Ensure it isn’t boiling — only a gentle simmer. If serving with croutons, prepare at this time (see notes below).
To incorporate the miso, add it separately to a small dish and top with ~1/4 cup of the warm broth. Use a spoon or whisk to fully combine, ensuring there are little to no clumps. Then add back to the pot and turn off heat (this ensures you don’t cook the miso, which would dampen its nutritional benefits). Stir to combine.
Taste and adjust flavors as needed, adding more salt or pepper to taste, coconut aminos for depth of flavor, or miso for umami flavor.
Serve hot topped with toasted croutons (optional) and additional herbs and black pepper. Store cooled leftovers in the refrigerator up to 4-5 days, or in the freezer for up to 1 month. Store croutons separately (loosely covered) at room temperature up to 1-2 days.
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Notes
*To make croutons, slice desired amount of day-old bread (we like sourdough) into cubes using a serrated or bread knife (use scissors if your bread is difficult to slice with a knife). Add to a baking sheet and toss to coat with a little oil, salt, pepper, and garlic powder. Bake for 8-10 minutes at 400 degrees F (204 C), or until golden brown and toasty. If oil-free, omit the oil and dry roast with the recommended seasonings. They won’t get as browned, but they will still be crispy. *Nutrition information is a rough estimate calculated with avocado oil and without optional ingredients or croutons.