In a large skillet, heat the 1 tablespoon of olive oil over medium heat. Add the chopped shallots and sauté for about 2-3 minutes until they become translucent. Add the garlic and red chili flakes, cooking for an additional minute until fragrant.
Stir in the cherry tomatoes, orange bell pepper, and yellow bell pepper. Cook for about 5 minutes, allowing the tomatoes to soften and release their juices. Next, add the mushrooms and cook for another 3-4 minutes until they start to brown.
Pour in the 2 1/2 cups of vegetable broth and bring the mixture to a gentle boil. Once boiling, add the whole wheat linguine to the pan. Stir well to ensure the pasta is submerged in the broth.
Reduce the heat to a simmer and cover the skillet. Cook for about 10-12 minutes, stirring occasionally, until the pasta is al dente and most of the broth is absorbed. If the pasta is not fully cooked but the liquid is gone, add a splash more broth or water as needed.
Once the pasta is cooked, stir in the chopped spinach, fresh basil, lemon juice and zest, sea salt, and black pepper. Mix until the spinach wilts and everything is well combined.
Remove the skillet from heat and sprinkle the grated Parmesan cheese over the top. Give it a gentle toss to incorporate the cheese, then serve immediately while hot, garnished with extra basil if desired.
