This Individual Vegetarian Shepherd’s Pie recipe with butternut squash topping is a delicious fall-veggie-packed comfort food meal. A savory sauté of lentils, mushrooms, spinach and tomatoes is spooned into individual ramekins and topped with golden pureed butternut squash and melted Gruyere cheese. They are naturally gluten-free and grain-free, they have 12 grams of protein, and they are only 229 calories each!

Vegetarian Shepherd’s Pies with Butternut Squash | gluten free | grain free | comfort food | Healthy Seasonal Recipes

Why We Love These Individual Vegetarian Shepherd’s Pie

When the craving for a hearty vegetarian recipe hits our family, we frequently gravitate to this easy individual vegetarian shepherd’s pie recipe. To us, it’s the perfect personalized, all-in-one dish that is so satisfying, you don’t even miss the meat!

This shepherd’s pie with butternut squash topping recipe is a fun twist on a classic. While the traditional UK version calls for minced lamb, this unique twist calls for hearty lentils, filling veggies, sweet butternut squash, and nutty Gruyere cheese.

And while we know many of you may be intimidated to make shepherd’s pie, we’re here to tell you that this recipe is simple, uncomplicated, and so delicious. It’s the perfect recipe when you want a healthy, delicious, all-in-one meal that’s tasty any time of the year.

What Is Shepherd’s Pie?

Shepherd’s Pie is a comforting casserole that originated in Scotland and quickly became a popular dish in Northern England and Ireland. Originally topped with a pastry crust, the Irish added their twist to this decadent dish and began to top this casserole with mashed potatoes as we know it today. Shepherd’s Pie is now a St. Patrick’s Day staple in the UK and the US.

This savory meat pie is full of sweet vegetables, a rich gravy, and topped with creamy mashed potatoes. The casserole is browned in the oven to form a crispy crust-like topping that is irresistible.

And over here, we love Shepherd’s Pie! We’ve made a Chicken Shepherd’s Pie with rotisserie or leftover chicken, a Healthy Shepherd’s Pie that’s low in calories and gluten-free, and a Lentil Shepherd’s Pie that showcases the traditional flavors of this comforting dish but swaps protein-packed lentils for meat! 

Key Ingredients For This Recipe


Lentils are an excellent easy vegetarian protein source. While this recipe can be made using 1 1/2 cups of cooked brown or green (i.e., French or de Pouille) lentils, no red as they are too mushy, we find that using canned lentils in this recipe works very well and slightly cuts down on the cooking time.

Vegetables: Mushrooms, Onion, Spinach

  • Mushrooms: We recommend using white mushrooms as they are readily available in most grocery stores and farmers markets and have a very mild flavor. When purchasing, purchase mushrooms that are smooth, firm, and dry. Avoid buying mushrooms that are slimy, soft, and brown spots as they are already past their prime.
  • Onion: We recommend using a diced sweet onion but feel free to use white.
  • Spinach: We also recommend using pre-packed baby or full-sized spinach as it is normally triple washed, so it only needs a quick rinse and spin before adding it to the lentil mixture. And no matter if you are using baby or full-sized, be sure to finely chop before adding it to the recipe.

Fruits: Roma Tomatoes and Butternut Squash

  • Roma Tomatoes: A plum variety of tomato that with a dense flesh and less juice, Roma Tomatoes help thicken the lentil mixture broth. When buying, look for tomatoes that have a consistent deep red color around the fruit, heavy for their size, with a strong sweet tomato smell.
  • Butternut Squash: A winter fruit that has a sweet, nutty flavor similar to pumpkin. When purchasing, choose a squash that is dark beige in color with a matte finish and a thick-hard skin. An easy test to see if a squash is good, gently prick the skin with your nail, if the nail pierces the skin, pick a different squash.


Note that we recommend table salt for this recipe. You may use kosher salt instead, but you will want to double the amount.

Vegetable Broth

Vegetable broth adds a deep savory element to the gravy. Our favorite brand is Imagine No Chicken as we find the taste superior to other brands in that it is not bitter or dark. However, feel free to use your favorite store-bought vegetable broth.


Used as a topping, Gruyere adds an additional richness to this already decadent dish. While I prefer the salty nutty notes of this hard cheese, feel free to substitute Swiss, Fontina, Raclette, Jarlsburg, or Emmental cheese.

Additional Ingredients

  • Organic olive or avocado oil
  • Fresh oregano
  • Unsalted butter
  • Greek yogurt

Step-By-Step Instructions To Make This Recipe

Step 1: Preheat Oven And Prepare Ramekins

Preheat oven to 375°F. Line a baking sheet with foil and place 6 large ramekins on top. Light coat the ramekins with cooking spray. Set aside.

Step 2: Prepare Lentil Mixture

In a large heavy skillet, heat oil over medium-high heat. Add onion, mushrooms, oregano, and ½ teaspoon salt. Cook and occasionally stir until the veggies begin to brown, about 10 minutes. Add lentils, spinach, and tomatoes and bring to a simmer. Remove from heat and divide amongst the prepared ramekins. 

Step 3: Prepare Butternut Squash Topping

Meanwhile, in a large saucepan fitted with a steamer attachment, bring 1-inch of water to a boil. Add squash to the steamer, cover, and cook until squash is fork-tender, about 12 -14 minutes. Pour squash into a food processor. Add butter, yogurt, and remaining ½ teaspoon salt. Puree until smooth. Divide the squash topping over the lentil mixture.

Step 4: Bake and Serve

Evenly top the healthy shepherd’s pie with cheese. Bake until the pies are bubbling, and cheese is melted for 10 – 15 minutes. Allow pies to slightly cool prior to serving.

Vegetarian Shepherd’s Pies with Butternut Squash | gluten free | grain free | comfort food | Healthy Seasonal Recipes

FAQ And Expert Tips

How do I store leftovers?

Leftover individual vegetarian shepherd’s pie can be stored it in an airtight container, or tightly wrapped in plastic wrap, in the refrigerator for up to 5 days.

Can vegetarian shepherd’s pie with butternut squash be made ahead of time?

Of course – this dish is a perfect make-ahead meal! To make ahead, prepare through step 3. Cover with foil and place in the refrigerator for up to 2 days. When ready to serve, top with cheese and cook according to recipe, keeping in mind that the dish may need any extra 10 to 15 minutes to warm all the way through.

What is a cottage pie?

A Cottage Pie is very similar to a Shepherd’s Pie; however, the filling is made with a minced beef filling versus lamb and the gravy is made from a broth versus the juices from the lamb. Like Shepherd’s Pie, it includes a mixture of sweet veggies, a velvety gravy, and is topped with a thick layer of mashed potatoes and baked until golden brown.

And while the title of this recipe is shepherd’s pie, this dish is technically a cottage pie as the gravy has a broth base versus a gravy made from the juices of minced lamb.

Additional Lentil and Butternut Recipes To Try

  1. This sneaky Vegan Lentil and Walnut Pate is incredibly rich and 100 percent plant based. You can add it to a Vegan Charcuterie board, or simply serve it with baguette. 
  2. This is hands down Best Vegetarian Lentil Soup and you’ll crave it again and again!
  3. Our Black Lentil Salad with Veggies and feta has a Mediterranean flair and delicious Walnut Vinaigrette.
  4. This Green French Lentil and Bacon dish is one I have been enjoying for years and pairs beautifully with Baked Salmon in Foil.
  5. The combination Celery Root and Lentil Salad comes together with a lemon, anchovy and herb dressing that is to-die-for!
  6. These Lentil Quinoa Bowls with Lemon and Coriander are an easy and tasty vegetarian Buddha Bowl.
  7. Easy Roasted Butternut Squash is a delicious vegan, paleo, and gluten-free recipe that only requires 10 minutes of hands-on prep!
  8. Butternut Squash Lasagna is a delicious vegetarian twist the classic. This impressive meal for guests can be made two days ahead of time and just popped in the oven before arrival!
  9. Traditional macaroni and cheese gets a healthy makeover in this Butternut Squash Mac and Cheese recipe! Made with whole-grain pasta, gruyere cheese, rosemary, and loaded with sweet butternut squash; making this a perfect comfort food casserole that everyone will enjoy!
Vegetarian Shepherd’s Pies with Butternut Squash | gluten free | grain free | comfort food | Healthy Seasonal Recipes

At Healthy Seasonal Recipes, we specialize in cooking with fresh veggies and creating weeknight meals. Sign up HERE to get more produce-forward dinner ideas for FREE! If you make this recipe, please come back and leave a star rating and review. I would love to hear what you thought! Happy Cooking! ~Katie

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Vegetarian Shepherd’s Pies with Butternut Squash | gluten free | grain free | comfort food | Healthy Seasonal Recipes

Individual Vegetarian Shepherd’s Pie with Butternut Squash

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5 from 6 reviews

  • Author: Katie Webster
  • Total Time: 1 Hour 15 Minutes
  • Yield: 6 servings 1x


These individual vegetarian shepherd’s pies with butternut squash topping are a delicious fall-veggie-packed comfort food meal. They are naturally gluten-free and grain free, they have 12 grams of protein and they are only 229 calories each!


  • 1 tablespoon organic canola oil or avocado oil
  • 1 large sweet onion
  • 1 cup chopped mushrooms
  • 1 tablespoon chopped fresh oregano or marjoram
  • 1 teaspoon salt, divided
  • 1 15-ounce can lentils, drained and rinsed (or 1 ½ c cooked lentils)
  • 1 packed cup finely chopped spinach or chard leaves
  • 1 large Roma tomato, chopped (about 1 cup)
  • ½ cup water or vegetable broth
  • 1 medium butternut squash, peeled, seeded and cut into large chunks
  • 2 tablespoons unsalted butter
  • ¼ cup plain Greek yogurt
  • 4 ounces shredded Gruyere cheese


  1. Preheat oven to 375°F. Line a baking sheet with foil. Set 6 large ramekins on the baking sheet. Coat lightly with cooking spray.
  2. Heat oil in a large heavy skillet over medium-high heat. Add onion, mushrooms, oregano or marjoram and ½ teaspoon salt, and cook, stirring occasionally until the vegetables start to brown, about 10 minutes. Add lentils, spinach, tomatoes and broth and bring to a simmer. Remove from the heat and divide among the prepared ramekins.
  3. Meanwhile, bring 1 inch of water to a boil in a large saucepan fitted with a steamer attachment. Add squash to the steamer, cover and cook until the squash is tender with pierced with a fork, 12 to 14 minutes. Empty squash into food processor. Add butter, yogurt and the remaining ½ teaspoon salt. Puree until smooth, scraping the sides of the processor as necessary. Divide the squash over the lentil mixture in the ramekins.
  4. Top the shepherd’s pie with cheese, dividing evenly. Bake until the pies are bubbling, and the cheese is melted, 10 to 15 minutes. Cool slightly before serving.
  • Prep Time: 45 minutes
  • Cook Time: 30 minutes
  • Category: Main Course
  • Method: Stove Top and Oven
  • Cuisine: American


  • Serving Size: 2 cups
  • Calories: 229
  • Sodium: 531 g
  • Fat: 13 g
  • Saturated Fat: 6 g
  • Carbohydrates: 19 g
  • Fiber: 6 g
  • Protein: 12 g