Pepitas Cilantro Pesto With Vegetable Noodles

Looking for a healthy and delicious pasta alternative? These butternut squash noodles with pepita cilantro pesto are packed with nutrients, flavor, and texture. A perfect low-carb, gluten-free, and plant-based dish that’s quick to prepare and satisfying for the whole family!

As a nutrition consultant and chef, I love transforming simple ingredients into vibrant, nutrient-packed meals. One of my favorite ways to swap out traditional pasta is with vegetable noodles—they’re colorful, light, and packed with vitamins. Plus, they’re a great way to use up leftover veggies in your fridge!

If you’re a fan of traditional basil pesto, you’ll love this cilantro pepita pesto. It’s a bright, nutty, and flavorful twist using toasted pepitas instead of pine nuts, making it both budget-friendly and full of essential minerals like magnesium and zinc. Pair it with spiralized butternut squash for a perfect side dish or toss it into grain bowls, pasta dishes, or bean salads for extra flavor. This is one great recipe to have in your back pocket!

Why You’ll Love This Recipe

This butternut squash noodle recipe is a great way to enjoy a healthy, satisfying meal without the heavy carbs. Here’s why it stands out:

• Nutrient-Dense & Low-Carb: If you love pasta but want something lighter and easier on digestion, butternut squash noodles are the perfect alternative. Packed with fiber, vitamin A, and antioxidants, they support gut health, glowing skin, and immune function, all while being naturally gluten-free and low in carbs.

• Homemade Pesto Magic: Forget store-bought pesto! This pumpkin seed cilantro pesto is creamy, nutty, and bursting with zesty lime juice. It’s loaded with healthy fats, magnesium, and essential nutrients that help balance hormones and reduce inflammation—all while being absolutely delicious!

• Easy & Quick to Make: This dish comes together in about 7-9 minutes. Perfect for busy weeknights or when you need a quick, healthy meal without spending hours in the kitchen.

• Perfect Topping for Everything: This cilantro pepita pesto isn’t just for noodles! Spoon pesto over grilled chicken, season salmon fillets, or drizzle on roasted vegetables for an instant flavor boost. You can also toss it into bean salads, grain bowls, or even spread it on toast.

Meal Prep Friendly: If you love meal prepping, this is a great recipe to have in your rotation. Store leftovers in an airtight container for up to 3 days, or freeze small portions in ice cube trays so you always have a flavorful, homemade pesto ready to go. Simply pop out a cube, thaw, and toss with your favorite dish!

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Ingredients For Pepita Pesto

Butternut Squash Noodles

Cylindrical squash (butternut squash) – A naturally sweet and slightly nutty vegetable perfect for spiralizing.

Cherry tomatoes, sliced in half (optional) – Adds a burst of freshness and color.

Fresh cilantro leaves and toasted pepitas, for garnish – Adds texture and a bright, herby finish.

Pepita Cilantro Pesto

Toasted pepitas (pumpkin seeds) – Gives a nutty flavor and a crunchy texture.

Garlic cloves, chopped – Adds a bold, savory kick.

Fresh cilantro leaves – The star ingredient for a fresh, vibrant, and slightly citrusy flavor.

Olive oil (or cup oil of choice) – Provides richness and blends the pesto smoothly.

Freshly squeezed lime juice (or lemon juice) – Brightens the flavors and adds acidity.

Nutritional yeast – A plant-based alternative to cheese with a savory, umami flavor.

Parmesan cheese (optional) – For a creamier, more traditional pesto taste.

How to Make It

1. Prepare the Butternut Squash Noodles: Select a butternut squash with a long neck for easier spiralizing. Cut off the round, seedy base and set it aside for another use, like soup or roasting. Using a vegetable peeler, remove the outer skin. If you have a spiralizer, create thin, noodle-like strands. Alternatively, you can use a vegetable peeler to make long, ribbon-like noodles. Once spiralized, pat the noodles dry with paper towels to remove excess moisture, which helps them cook evenly.
2. Make the Pepita Cilantro Pesto: In a large nonstick skillet, toast the pumpkin seeds over medium heat for about 5 minutes, stirring occasionally, until they become fragrant and slightly golden. Transfer them to a food processor, then add garlic, fresh cilantro, olive oil, lime juice, nutritional yeast, parmesan cheese (if using), salt, and black pepper. Pulse the mixture until a coarse purée forms, scraping down the sides as needed. If the consistency is too thick, add a splash of water and blend again until smooth.
3. Cook the Noodles: Heat olive oil in a large nonstick skillet over medium-high heat. Add the butternut squash noodles in batches, making sure not to overcrowd the pan. Stir gently, cooking for about 7-9 minutes or until the noodles are tender but still slightly firm (al dente texture). Transfer the cooked noodles to a mixing bowl, reserving the skillet for any additional toppings.
4. Serve & Garnish: Toss the warm noodles with the pepita cilantro pesto, gently massaging it in so the flavors coat every strand. Plate the noodles and top with cherry tomatoes, extra cilantro, and toasted pepitas for added texture and color. Sprinkle it with parmesan cheese or nutritional yeast for an extra layer of flavor. Finish with black pepper, flaky salt, and a squeeze of lime wedges on the side for a bright, zesty touch.

Ingredient Substitutions

• Butternut Squash: Swap with zucchini, sweet potatoes, or carrots for variety.
• Pepitas: Use pine nuts, sunflower seeds, or almonds if needed.
• Cilantro: Replace with basil or parsley for a different flavor.
• Nutritional Yeast: Use parmesan cheese if not vegan.

Health Benefits for Women’s Health

This dish is packed with nutrients that support women’s health in so many ways. Butternut squash is a great source of vitamin A and fiber, which promote gut health, radiant skin, and hormonal balance. Fiber supports digestion and helps maintain stable blood sugar levels, which is crucial for hormone regulation.

Pumpkin seeds are loaded with magnesium and zinc, two key minerals that aid in hormone production, reduce inflammation, and improve sleep quality. These nutrients also play a role in stress management and reproductive health. While cilantro helps detoxify the body by removing heavy metals and toxins, which can interfere with hormone function. It also has antioxidant properties that support overall well-being.

Olive oil is rich in monounsaturated fats, which contribute to heart health, brain function, and hormone balance. These healthy fats help reduce inflammation and improve circulation, ensuring your body functions optimally.

Chef Tips

For the best results, always use fresh, high-quality ingredients. The flavors of this dish shine when using fresh cilantro, high-quality olive oil, and freshly toasted pepitas. When cooking the butternut squash noodles, be careful not to overcook them. They cook quickly, so stir gently and cook for just 7-9 minutes to maintain an al dente texture.

If the pesto is too thick, simply add a splash of water or more olive oil to reach your desired smoothness. For an even deeper flavor, toast the coriander seeds before blending them into the pesto. 

Ways to Serve

This dish is incredibly versatile and pairs well with a variety of meals. Serve it over grain bowls or pasta dishes for a hearty, plant-based option packed with nutrients. The creamy pepita cilantro pesto adds a rich depth of flavor, making it a perfect complement to quinoa, brown rice, or even whole wheat pasta. For a protein-packed meal, enjoy these butternut squash noodles alongside seasoned salmon fillets. The natural sweetness of the squash balances beautifully with the richness of the fish, creating a satisfying, well-rounded dish.

Storage

To keep your leftovers fresh, store them in an airtight container in the refrigerator for up to 3 days. The butternut squash noodles may soften slightly over time but will still be delicious. For longer storage, freeze the pepita cilantro pesto in ice cube trays for easy portioning. Simply pop out a cube and let it thaw before using it in your next meal, ensuring you always have a quick, flavorful topping ready to go.

Equipment

1. Spiralizer or vegetable peeler
2. Food processor
3. Large nonstick skillet
4. Baking sheet
5. Paper towels

Frequently Asked Questions

Can I make this pesto ahead of time?

Yes! Store in an airtight container in the fridge for up to 3 days or freeze in ice cube trays for easy portioning.

Can I use a different nut or seed for the pesto?

Absolutely! Pine nuts, sunflower seeds, or almonds work great as substitutes for pepitas.

How can I make the noodles softer?

If you prefer a softer texture, cook the butternut squash noodles for an additional 2-3 minutes, stirring frequently.

What’s the best way to reheat leftovers?

For the best texture, reheat the noodles in a skillet over medium heat for a few minutes instead of microwaving.

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