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Combine lukewarm water, yeast, and honey in a small bowl and set in a warm place to proof for 10 minutes. Meanwhile, whisk to combine 2 cups spelt flour and sea salt in a large mixing bowl.
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After 10 minutes, yeast mixture should be bubbly with a foamy layer on top. Fold yeast mixture into dough with a spatula. Knead dough and add remaining spelt flour as needed until dough is pliant but not sticky. (I used 3 tablespoons more.) Drizzle in olive oil and knead to incorporate into dough. Knead dough about 4 minutes or until the surface is smooth and dough is stretchy. Cover bowl loosely with plastic wrap and then with a warm, moist towel, and set in a warm, draft-free place to rise until dough has doubled in size, 60 - 90 minutes.
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While dough rises, begin to caramelize the shallots. First, heat 2 tablespoons olive oil over medium heat in a medium-sized skillet. Add shallots and a pinch of sea salt, and cook just until they start to sizzle. Stir and turn heat to low. Continue cooking, stirring every 10 minutes or so, until shallots are a rich golden hue and the edges have crisped, about 50 minutes.
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Move rack to top of oven. If using a pizza stone position on the top rack. Preheat oven to 475 degrees F. (Oven should preheat at least 30 minutes.)
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When dough has doubled in size, turn out onto a lightly floured surface and divide into 8 pieces. Roll or pat each piece into a disc, then roll into a 6-inch round on a lightly floured piece of parchment. Layer the rolled pizza dough discs between parchment on a large plate, cover with a towel and set aside to rest for 20 minutes.
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Meanwhile, prep topping and make pesto. For pesto, pulse to combine greens, parsley, green onion, lemon zest, and pepitas. With machine running, drizzle in olive oil just until combined. Finally, add 1 tablespoon lemon juice and sea salt to taste.
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Lay out toppings: pesto, grated cheese, sliced green onions, asparagus, and cauliflower. Crispy shallots should be added to pizzas after they've cooked.
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To assemble pizzas, take a sheet of parchment with a rolled pizza dough disc and spread 1 - 2 tablespoons pesto, leaving a 1/2-inch gap for the crust. Add cheese and toppings of choice. Lay pizza and its parchment on the hot pizza stone and bake until cheese is bubbling and edges are crisp, 6 - 8 minutes.
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Cool, slice, and serve.