Heat 1 tablespoon of oil in a large nonstick skillet over medium heat. Add the gnocchi and spread it out into one even layer. Cook, stirring occasionally (about every 2 minutes), until it's golden brown on all sides, about 12 to 15 minutes. Transfer the gnocchi to a bowl or plate and set aside.
Add the remaining 1 tablespoon of oil to the same skillet. Sauté the onion until soft and translucent, about 4 minutes.
Add the garlic, Italian seasoning, salt, pepper, red pepper flakes, and nutmeg. Stir and cook until fragrant, about 1 minute.
Add the butter. Stir to incorporate until melted. Sprinkle the flour over the top of the onion mixture. Stir until no white flour remains visible, about 1 minute.
Slowly add the non-dairy milk, whisking continuously to prevent lumps.
Add the frozen spinach and nutritional yeast and stir to combine. Increase the heat to bring to a boil, then decrease the heat to medium-low and simmer until the sauce is thickened, about 10 minutes. Use a wooden spoon to break up any clumps of spinach as it's simmering.
Return the gnocchi to the skillet, add the lemon juice, and stir until it is completely coated in the creamy spinach sauce. Taste and adjust seasoning as necessary.
Serve immediately.