Preheat the oven to 450°F.
Heat a large nonstick skillet over medium heat and spray with cooking spray. Sauté the shallots and garlic until tender; season with salt and pepper. Add the mushrooms and sauté until they have released their liquid and turn a deep golden brown. Stir in the spinach until incorporated. Remove from the heat.
Spray four 8-ounce ramekins with cooking spray. Divide the spinach mixture among the ramekins and carefully break 3 eggs into each. Place the ramekins on a baking sheet and bake until the whites of the eggs are set and the yolks are still runny, 7 to 10 minutes.
Toast the English muffins and drizzle with flaxseed oil. Serve each person one ramekin and half an English muffin.