Cheesy Lentil Stuffed Spaghetti Squash (Vegan)
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Cheesy Lentil Stuffed Spaghetti Squash

Comforting, wholesome, and delicious, vegan cheesy lentil stuffed spaghetti squash. The perfect healthy fall inspired dinner.

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Comforting, wholesome, and delicious, vegan cheesy lentil stuffed spaghetti squash. Rich flavors of a perfectly baked lasagna, but made a little healthier by swapping out regular pasta with seasonal spaghetti squash. The spicy lentils transform this squash recipe into a meatless, meaty dinner dish. Top each lentil-stuffed spaghetti squash with a simple vegan garlic-thyme infused cheese sauce. Bake everything together, and then serve with fresh thyme and basil leaves. This spaghetti squash bake feels like a warm hug, packed with all those fall spices we love. Make this on nights you’re craving pasta, but want something healthier!

This cheesy lentil stuffed spaghetti squash recipe is a…

  • great thanksgiving main dish or even side dish!
  • flavorful dish.
  • comforting dinner.

Ingredients for vegan lentil spaghetti squash

  • Spaghetti squash: You’ll need 2 spaghetti squashes. Once baked, it’ll transform into squash noodles which is a great healthy alternative to pasta. The squash flesh holds all the ingredients together, making this recipe kinda like vegan lasagna bowls, but without the bowls.
  • Lentils: This will be one of the star ingredients for this recipe. I made the lentils from scratch, but to save time use canned lentils!
  • Onion: Just one yellow onion, sliced or diced.
  • Garlic: Grated garlic for the vegan cheese sauce but also for the spicy lentils.
  • Fresh herbs: Thyme leaves for the vegan cheese sauce, and basil leaves for serving!
  • Spices: Chili flakes (or chili powder), ground nutmeg, ground cinnamon, dried basil, salt and black pepper.
  • Tomatoes: A little tomato paste (aka puree), and tinned chopped tomatoes for the spicy lentils.
  • Maple syrup: Just a dash to sweeten things up a little.
  • Vegan cheese: Grated vegan cheese to make the garlic-thyme infused cheese sauce. You could also grate a little vegan parmesan over the squash before baking too!
  • Non-dairy milk: Use any plant milk of your choice! I used oat milk, but almond milk, soy milk, rice milk will work perfectly.
  • Flour: Just a few tablespoons to thicken up the vegan cheese sauce.
  • Vegan butter: I use salted, but unsalted will work too. Or you could simply use more olive oil instead.
  • Olive oil: It’ll be used to roast the spaghetti squash and to make the lentil sauce.

All about spaghetti squash…

Spaghetti squash is a fall/winter seasonal veg that transforms into a spaghetti-like texture once baked! 

All types of squash can be a little hard to slice, so to make this easier (and safer), I like to pop the whole spaghetti squash into the microwave and heat it for a minute or two. Doing this will soften up the squash a little. Then with a sharp knife, slice the spaghetti squash in half. Scrape out all the seeds from the inside with a spoon.

Repeat with the second squash. Place the squash halves onto a baking sheet with the cut side facing up, drizzle with olive oil, and sprinkle over a pinch of salt and black pepper. It’s crucial to season the squash a little before baking because this is the only time we’ll be able to season the inside flesh! Next, bake for 15 minutes.

The protein-packed lentil sauce…

While the spaghetti squash cooks, start making the lentil layer. The spicy lentils are the star of this recipe. Lentils have this hearty texture that makes the perfect substitute for store-bought vegan meat alternatives. Plus, it makes it a little healthier too. It’s also packed with protein and super comforting. The lentil sauce is a thick marinara sauce that’s loaded with fall spices.

To start you can either use ready-cooked canned lentils or boil a batch yourself. If you choose to boil your own, you’ll need around 1 cup. Place it into a pot with cold water, bring to a boil, and cook for 8-10 minutes or until the lentils are cooked. Drain out the water and set it aside. 

In the same pot, the lentils were cooking in, add olive oil and heat over medium heat. Add in the onions and cook until they start to get a little golden. Mix in the grated garlic, chili flakes, salt, black pepper, cinnamon powder, nutmeg powder and dried basil. Cook together for just 1 minute. At this point, your home will be filled with all those warm, fall flavors we all love. Add in the tomato purée and while consistently mixing, cook for 3-4 minutes. 

Mix in the cooked lentils and tinned chopped tomatoes. Cook together with all those warm spices for 4-6 minutes. Turn off the heat and set aside. 

Making the creamy, garlic-thyme infused cheese sauce…

This cheese sauce gifts this spaghetti squash recipe with a lovely, thick and creamy sauce that’s infused with garlic and thyme! YUM. It really transforms this simple spaghetti squash bake into something incredible.

Add the vegan butter, garlic and thyme leaves to a pan. Heat everything together over medium-high heat. Once the butter melts, allow it to cook for a few extra seconds. Add in the flour and cook for 1-2 minutes while consistently mixing to prevent the flour from burning. Once the mixture becomes thick, slowly steam in the oat milk, and with your other hand mix everything together. At this point, the cheese sauce will be thick. Add in the vegan cheese and as soon as most of the cheese has melted turn off the heat. 

Final touches…

Divide the spicy lentils between all 4 halves of the half-baked spaghetti squash. Dollop over that garlic-thyme-infused cheese sauce. Spread it over using the back of a spoon. Bake everything together for another 20 minutes or until the vegan cheese sauce starts to get a little golden on top. 

Transforming this squash into a healthy spaghetti alternative is my favorite part! Simply grab a fork and scrape the insides of the squash. You’ll see very quickly how simple and fun it is! The combination of noodly spaghetti, lentils with a meaty texture and garlic-thyme infused cheese sauce is delicious! Replacing traditional pasta might seem scary but give this recipe a try! It’ll easily become one of your favorite healthyish recipes to make. You can for sure have one-half of spaghetti squash per person, but you might want to cut those halves into smaller portions. Serve this delicious stuffed spaghetti squash with a little fresh basil and a glass of wine.

Store any leftovers in an airtight container and keep them refrigerated for 2-4 days. It’ll actually taste even more incredible the next day.

Once you try this vegan cheesy lentil-stuffed spaghetti squash recipe, please leave a star rating and review below! I try my best to respond to you all. Oh, and don’t forget to tag me on Instagram – I can’t wait to see your images!!

More vegan recipes you’ll love…


Cheesy Lentil Stuffed Spagetti Squash

Comforting, wholesome, and delicious, vegan cheesy lentil stuffed spaghetti squash. The perfect healthy fall inspired dinner.

  • Prep Time: 20 minutes
  • Cook Time: 1 hour
  • Total Time: 1 hour
  • Yield: 8 people 1x
  • Category: Main Course
  • Cuisine: American, Italian
image of vegan cheesy lentil stuffed spaghetti squash recipe
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Units Scale


  • 2 spaghetti squash (halved and seeds removed)
  • 2 tbsp olive oil
  • 1 onion (sliced)
  • 34 garlic cloves (grated)
  • 1 tsp dried basil
  • 12 tsp chili flakes
  • 1/4 tsp ground cinnamon
  • 1/2 tsp ground nutmeg
  • salt + black pepper
  • 4 tbsp tomato puree/ paste
  • 1 cup chopped tinned tomatoes
  • 2 cups cooked lentils
  • 2 tsp maple syrup

Garlic-Thyme Infused Cheese Sauce

  • 6 tbsp all-purpose flour
  • 6 tbsp vegan butter or olive oil
  • 3 garlic cloves (grated)
  • 1 cup oat milk
  • 2 cups grated vegan cheese
  • 1 tbsp fresh thyme leaves
  • salt + black pepper


  1. Pre-heat oven 220°C/425°F
  2. Spaghetti squash: Drizzle with a little olive oil, and sprinkle with salt and black pepper. Bake for 15 minutes.
  3. Spicy Lentils: Heat oil in a pan over medium heat. Add in the onions, and cook until they start to become a little golden. Mix in the grated garlic, chili flakes, salt, black pepper, cinnamon powder, nutmeg powder and dried basil. Cook for 1 minute. Add in the tomato puree and cook for 3-4 minutes while consistently mixing. Mix in the cooked lentils, tinned tomatoes and maple syrup. Cook for 4-6 minutes.
  4. Garlic-thyme infused cheese sauce: In a pan heat vegan butter, garlic and thyme leaves over medium-high heat. Once the butter has melted, cook for a further minute. Add in the flour, and cook for 1-2 minutes while consistently mixing. Slowly stream in the oat milk, and mix everything with your other hand. Add grated vegan cheese to the thick mixture. Once most of the vegan cheese has melted, turn off the heat. Season with a little salt and black pepper.
  5. Final touches: Add the spicy lentils to each spaghetti squash. Top with the thick vegan cheese sauce, and with the back of a spoon spread it over the lentils. Bake for 15-20 minutes or until the vegan cheese sauce is golden. Use a fork to pull out the noodle-like spaghetti texture. Enjoy with a bit of fresh basil!