Heat a large skillet over medium heat and add the olive oil.
Add the chopped shallot and sauté until soft and translucent, about 5 minutes.
Add the minced garlic, nutritional yeast, fennel seeds, smoked paprika, dried oregano, and red pepper flakes; cook, stirring, for about 1 minute until fragrant.
Stir in the cooked lentils and chopped broccoli rabe; season with salt and pepper.
Add the gnocchi, vegetable stock, and non-dairy milk; stir to combine and submerge the gnocchi and vegetables in the liquid, adding more stock if needed.
Bring to a boil, then reduce heat and simmer for about 5 minutes, stirring occasionally, until the gnocchi are tender.
Add the frozen peas and vegan pesto, stir to combine, and simmer until peas are tender and bright green, about 2 minutes.
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.