Healthy Baked Lentil Marinara Spaghetti Squash

If you’re looking for a hearty yet wholesome dinner, this Baked Lentil Marinara Spaghetti Squash is a game-changer.

It combines fiber-rich spaghetti squash with protein-packed lentils, delivering a satisfying plant-based twist on classic pasta.

With fewer carbs, plenty of nutrients, and a comforting Italian-inspired flavor, it’s a smart choice for everyday cooking.

Easy, filling, and family-friendly, it’s perfect for weeknights or meal prep.

Baked Lentil Marinara Spaghetti Squash

Karina Kari
A hearty yet healthy Italian-inspired bake featuring roasted spaghetti squash topped with a rich lentil marinara sauce and melted Romano cheese.
High in fiber, protein-packed, and naturally gluten-free, this dish is a satisfying low-carb alternative to traditional pasta.
Prep Time 10 minutes
Cook Time 1 hour
Total Time 1 hour 10 minutes
Course dinner
Cuisine Italian
Servings 4

Equipment

  • 1 Sharp Chef’s Knife
  • 1 large baking sheet
  • 1 medium saucepan
  • 1 Food processor (or blender)
  • 1 9×13-inch baking dish
  • 1 wooden spoon
  • 1 cheese grater

Ingredients
  

  • 1 large spaghetti squash about 6–7 cups cooked
  • 1 cup dried green lentils
  • 2 cups water for cooking lentils
  • 1 can 14.5 oz diced tomatoes
  • ½ cup tomato paste
  • ½ cup finely chopped red onion
  • 1 –2 garlic cloves minced
  • 1 teaspoon dried parsley or fresh, chopped
  • 1 teaspoon dried oregano
  • 1 teaspoon Italian seasoning
  • 1 teaspoon smoked paprika
  • ½ teaspoon sea salt
  • ¼ teaspoon black pepper
  • teaspoon crushed red pepper optional
  • 3 oz freshly grated Romano cheese
  • Fresh parsley for garnish

Instructions
 

  • Preheat the Oven: Begin by heating your oven to 400°F (200°C).
    This ensures it’s fully warmed up and ready to roast the spaghetti squash, which is the base of the dish.
    A properly preheated oven helps the squash cook evenly and develop a slightly caramelized flavor around the edges.
  • Prepare the Spaghetti Squash: Place the squash on a sturdy cutting board.
    Using a sharp chef’s knife, carefully slice it lengthwise from top to bottom.
    Scoop out the seeds and stringy pulp with a spoon, leaving only the clean, firm flesh.
    Arrange the squash halves cut-side up on a large baking sheet, with the skin side resting against the pan.
  • Roast the Squash Until Tender: Transfer the baking sheet to the preheated oven.
    Roast the squash for 45 to 50 minutes, or until the flesh can easily be pierced with a fork.
    When fully cooked, you should be able to drag a fork across the inside of the squash and pull up long, noodle-like strands that resemble spaghetti.
    Set aside to cool slightly once roasted.
  • Cook the Lentils: While the squash is roasting, place 1 cup dried green lentils and 2 cups of water into a medium saucepan.
    Bring to a boil over medium-high heat.
    Once boiling, reduce the heat to low, cover the pot, and simmer for about 30 minutes.
    The lentils should become soft and absorb nearly all the water.
    If a little liquid remains, simply drain it off.
  • Blend the Marinara Sauce: As the lentils cook, prepare the sauce.
    Add the following ingredients to a food processor or blender diced tomatoes, tomato paste, chopped onion, minced garlic, parsley, oregano, Italian seasoning, smoked paprika, sea salt, black pepper, and crushed red pepper (if using).
    Blend on high speed for 25 to 30 seconds, or until everything is fully combined into a thick, rich sauce.
    You should see a smooth consistency with no large chunks remaining.
  • Combine Lentils with Sauce: Once the lentils are fully cooked and tender, pour the blended tomato sauce into the saucepan with them.
    Stir thoroughly until the lentils are evenly coated and the sauce takes on a hearty, meat-like texture.
    Taste and adjust seasoning if needed—adding a pinch more salt, pepper, or herbs to suit your preference.
  • Assemble the Casserole Dish: Take a 9×13-inch baking dish (or a similar oven-safe dish).
    Using a fork, scrape the roasted squash flesh into long strands, then spread them evenly across the bottom of the dish.
    The strands should form a fluffy, pasta-like layer that covers the base completely.
  • Add the Lentil Marinara Layer: Spoon the lentil and marinara mixture over the bed of spaghetti squash, spreading it out so every bite will have a generous amount of sauce.
    Smooth the top with the back of your spoon, ensuring it covers the squash evenly.
  • Top with Cheese and Garnish: Sprinkle freshly grated Romano cheese across the top of the casserole.
    This adds a savory, salty richness that melts beautifully in the oven.
    Add a scattering of fresh parsley for color and brightness.
  • Bake Until Bubbly and Golden: Return the baking dish to the oven and bake for 15 minutes, or until the cheese has melted into the sauce and the dish is hot all the way through.
    You should see a light bubbling around the edges, signaling that it’s ready.
  • Rest Before Serving: Remove the dish from the oven and allow it to cool for about 5 minutes.
    This short rest time helps the layers set slightly, making it easier to serve neat portions without falling apart.
  • Serve and Enjoy: Scoop the casserole onto plates or into bowls.
    For extra flavor and presentation, top each serving with another sprinkle of Romano cheese and a few fresh parsley leaves.
    Serve hot and enjoy a comforting, hearty, and nourishing meal.

Notes

  • Spaghetti squash is a naturally gluten-free, low-carb pasta alternative.
  • Lentils add hearty texture and plant-based protein to replace meat.
  • Freshly grated Romano cheese melts better and tastes sharper than pre-shredded.
  • Roasting the squash cut-side up keeps it from becoming watery.
  • The blended sauce gives a smooth, restaurant-style marinara finish.
  • This dish can be assembled ahead and baked just before serving.
  • Optional crushed red pepper adds a gentle kick of heat.

Chef’s Secrets for Perfect Results

The key to success with this recipe lies in balancing texture and flavor.

Roasting the squash cut-side up prevents excess moisture and ensures strands that are firm but tender, resembling real pasta.

When cooking lentils, keep the water at a gentle simmer—boiling too vigorously can make them split and turn mushy.

For the sauce, blending the tomatoes with seasonings creates a smooth consistency that clings to the lentils beautifully, giving the dish a hearty “meat sauce” feel.

Using freshly grated Romano instead of pre-shredded cheese is another insider tip, as it melts more evenly and brings sharper flavor.

Serving Suggestions and Pairing Ideas

This baked spaghetti squash casserole makes a complete and filling meal on its own, but it pairs wonderfully with a crisp side salad dressed in balsamic vinaigrette or a platter of roasted vegetables for extra color and nutrition.

Garlic bread or toasted sourdough also makes a delicious companion, especially for those who want a mix of light and hearty textures at the table.

For beverages, try pairing with sparkling water infused with citrus for a refreshing touch, or a glass of red wine such as Chianti for an Italian-style dinner experience.

Storage Tips and Make-Ahead Options

Leftovers store well and taste even better the next day as the flavors meld together.

Allow the casserole to cool completely, then cover the baking dish tightly or transfer portions into airtight containers.

Refrigerate for up to 4 days.

To reheat, warm individual servings in the microwave or reheat in the oven at 350°F (175°C) until hot throughout.

For longer storage, freeze portions for up to 2 months.

To use as a make-ahead meal, you can assemble the dish through Step 9, refrigerate it, and bake just before serving for maximum freshness.

Frequently Asked Questions

1. Can I use red or brown lentils instead of green?

Green lentils work best because they hold their shape after cooking. Red lentils tend to become mushy, while brown lentils are softer but still usable if you prefer a creamier sauce texture.

2. How can I make this recipe vegan?

Simply omit the Romano cheese or replace it with a dairy-free alternative. Nutritional yeast also adds a cheesy, savory flavor without dairy.

3. Can spaghetti squash be cooked in the microwave?

Yes! For a quicker option, place the halved squash cut-side down in a microwave-safe dish with a little water. Microwave for 10–12 minutes, checking for doneness with a fork.

4. What can I use instead of Romano cheese?

Parmesan is a great substitute, offering a similar sharpness. For a milder option, try mozzarella, though it will give a creamier melt rather than a salty bite.

5. Is this dish suitable for meal prep?

Absolutely. It reheats very well, making it ideal for preparing in advance. Portion it into containers and refrigerate or freeze, then reheat as needed for quick, healthy lunches or dinners.