Heat a large skillet over medium heat and add the olive oil.
Add the chopped shallot and sauté until soft, about 4–5 minutes.
Stir in the minced garlic, nutritional yeast, fennel seeds, smoked paprika, dried oregano, and red pepper flakes; cook until fragrant, about 1 minute.
Add the cooked lentils and chopped broccoli rabe and toss to combine; season with salt and pepper.
Add the gnocchi, vegetable stock, and non-dairy milk; stir to submerge the gnocchi and vegetables, adding extra stock if needed.
Bring the mixture to a boil, then reduce to a simmer and cook for about 5 minutes, stirring occasionally.
Stir in the frozen peas and vegan pesto and simmer until the peas are tender and bright green, about 2 more minutes; the gnocchi should be tender but not gummy.
Stir in the lemon juice, taste and adjust seasoning with more salt, pepper, or lemon as desired.
Serve hot topped with chopped fresh basil and vegan parmesan.