by Olena

Healthy Chicken Pot Pie Casserole with Quinoa Crust

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Olena Osipov
5 from 17 votes

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Healthy Chicken Pot Pie Casserole has a creamy filling of veggies, juicy chicken, and the best flourless, cheesy, crunchy crust made with quinoa. This lighter version of a comfort food classic is so easy to make from scratch!

A piece of chicken pot pie on a plate with a fork garnished with fresh parsley.

Buckle up, friends, this healthy chicken pot pie casserole is even better than the original! It’s shed some pounds and feeling fabulous but just as chunky and creamy on the inside and that, my friends, is what counts 😉

This classic comfort food is chock full of veggies and tender pieces of chicken keeping it super cozy. Even with omitting butter, heavy cream, and canned soup, you will still have grandma’s seal of approval!

Healthy chicken pot pie with veggie filling of peas carrots and corn plated with a fork.

I came up with this casserole pie crust using Instant Pot quinoa which is a whole grain, a complete protein, and full of complex carbs. It’s crispy, cheesy, and crazy yummy. It also makes a great grain free crust for quinoa skillet with chicken and garden vegetables or black bean quinoa casserole.

This flourless chicken pot pie casserole, similar to one pot chicken quinoa, is ready in under 1 hour which makes it the perfect weeknight meal my whole family requests year round.

Healthy Chicken Pot Pie Ingredients and Substitutions

With a veggie packed filling, lightened up creamy sauce and gluten free crust this is a healthy pot pie casserole with no refrigerated pastry in sight!

Filling Ingredients

  • Cooked chicken breast. I usually use Instant Pot chicken breast. To make this casserole even easier, though, use leftover chicken breast! It can be baked chicken breast, grilled, or even leftover rotisserie chicken. In pinch, cooked ground chicken or chicken thighs also work.
  • Peas, corn and carrots. I used frozen peas and corn and then added chopped fresh carrot. Those three veggies are standard from scratch pot pie non negotiables in my opinion! Celery, onion, and mushrooms could also be added or you can also use a ready made mirepoix mix. Diced red or yukon gold potatoes are also popular pot pie casserole additions.
  • Seasonings. Thyme, garlic powder, salt, and pepper are all you need, but you could use onion powder and rosemary, too!
  • Oil and cooking spray. Any mild oil you use normally use for sauteing vegetables. Cooking spray is to help with nonstick to the dish, this helps especially when serving!

Sauce Ingredients

  • Milk. Although you can use any milk, including dairy free, whole milk makes the creamiest sauce. The higher the fat content the richer it will makes this healthy chicken pot casserole taste.
  • Chicken broth. I recommend my low sodium Instant Pot chicken stock, but store-bought works too. I will say there is something about the freshness of making everything from scratch with a homemade dish.
  • Cornstarch. This is used to thicken the filling. Arrowroot powder could be used for a paleo option or even flour in a pinch.

Crust Ingredients

  • Cooked quinoa. Using Instant Pot recipes speeds things up, so I usually end up making Instant Pot quinoa. If you prefer, I can show you how to cook quinoa on the stove instead. Leftovers can be used in this Mediterranean quinoa salad.
  • Cheese. I personally love mozzarella or cheddar cheese, but you can use what you’ve got. I always recommend grating your own fresh from a block because it makes such a difference!
  • Eggs: They act as a binder for the crust, which is important since we’re not using a typical pastry crust. I’ve never tried with an egg replacer, so I’d be interested to hear from anyone that does.
Frozen mixed vegetables cooked quinoa cheese cooked chicken onion broth eggs milk and seasonings to show ingredients.

How to Make Healthy Chicken Pot Pie Casserole

It may look complicated, but I promise if we break it down step-by-step, you will have this from scratch dish in the oven for dinner in no time. Preheat the oven, spray the casserole dish, it really is so easy!

Make Quinoa Crust Topping and Saute Filling

Whisk 3 eggs and combine with cooked quinoa, shredded cheese, and pepper. This will be your quinoa pot pie crust, set aside.

Make pot pie filling by first sautéing the onion and celery. You always want to cook onion before adding mushrooms because they are super watery and will steam rather than fry the onion. Add mushrooms and cook for 3 more minutes. Next, add the thyme, garlic powder, salt, pepper, peas, corn, and carrots.

Make Sauce

In a separate bowl, mix broth, milk, and cornstarch, this will be your slurry to thicken your chicken pot pie casserole sauce. Make sure the liquids are cold to start because cornstarch will lump in hot water.

Whisk the slurry again before adding it to the skillet. Simmer until your creamy sauce thickens and bubbles, then add cooked chicken. Turn off the heat.

Assemble and Bake

Once ingredients are cooked, assemble the pot pie. Use a regular large baking dish and pour your filling into it, then level with a spatula. Drop spoonfuls of quinoa crust all around evenly and spread with a spatula. It’s ok if some of the sauce bubbles on top of the crust. It will settle back inside during the cooling time. Poking the crust with a fork will minimize this. 

Bake casserole uncovered for 25 minutes in preheated oven at 375 degrees F. Remove from oven and let cool for 10-15 minutes. Cut into 8 squares, serve hot and enjoy!

Storing and Reheating

Store: Leftovers should be stored in the refrigerator in an airtight container for up to 3 days.

Reheat: Casserole can be reheated by popping back in the oven for 15 minutes at 400 degrees F.

Can You Freeze This Casserole?

Yes! There are two options when it comes to freezing this healthier pot pie.

Freeze unbaked casserole: How amazing are freezer meals? This one is as easy as pie to assemble as per the recipe and then cover it unbaked with plastic and foil. That’s it! Freeze it for up to 3 months and when you are ready to eat, thaw in the refrigerator overnight. Bake as per recipe instructions plus add an extra 15 minutes.

Freeze baked casserole: You can freeze chicken pot pie leftovers for up to 3 months in an airtight glass container. To thaw, just place on a counter and defrost for 3-4 hours.

Recipe FAQs

Is chicken pot pie healthy?

Typical chicken pot pie uses a double crust which often is a flaky pie crust, puff pastry dough, or a Bisquick mix crust. As delicious as they are those crusts are often processed, loaded with butter, and full of white flour. This healthier version just uses a crusty whole food quinoa topping plus lightened up with no heavy cream!

Why is my chicken pot pie runny?

It settles as it cools, so it could be that it is still too hot. It could also be that it needs more cook time to thicken up.

What to Serve It With

Chicken pot pie is already a complete meal but sometimes we’re extra hungry!

A simple baby kale salad or my favorite sweet kale salad adds extra veggies and bright colors to the dinner table.

Keep it low carb and grain free with cheesy cauliflower breadsticks or cauliflower mashed potatoes, both would be amazing!

Love the idea of turning comfort classics into healthy classics? Try my cauliflower shepherd’s pie and ground turkey meatloaf next!

More Healthy Casseroles

Healthy Chicken Pot Pie in baking dish with a square cut out showing chicken peas carrots and corn.
Healthy Chicken Pot Pie Casserole with Quinoa Crust

Healthy Chicken Pot Pie Casserole with Quinoa Crust

Healthy Chicken Pot Pie Casserole has a creamy filling of veggies, juicy chicken, and the best flourless, cheesy, crunchy crust made with quinoa. This lighter version of a comfort food classic is so easy to make from scratch!
5 from 17 votes
Print Save Rate
Course: Casserole
Cuisine: North American
Prep Time: 15 minutes
Cook Time: 35 minutes
Total Time: 50 minutes
Servings: 8 servings
Calories: 357kcal
Author: Olena Osipov


For the Crust:

  • 3 large eggs
  • 2/3 cups mozzarella or cheddar cheese shredded
  • 3 cups cooked quinoa stovetop or Instant Pot method

For Chicken Pot Pie Filling:


  • Preheat oven to 375 degrees F. Spray large 9 x 13 baking dish with cooking spray. Set aside.
  • In a medium bowl, whisk the eggs. Add cooked quinoa, cheese and pepper; stir with a spoon to combine and set aside.
  • In another medium bowl, make the slurry by combining chicken stock, milk, cornstarch and whisk with a fork. Make sure liquids are cold otherwise cornstarch will lump.
  • Preheat large ceramic non-stick skillet on medium heat and swirl oil to coat. Add onion and celery; cook for 5 minutes, stirring occasionally. Add mushrooms and cook for 3 more minutes.
  • Add thyme, garlic powder, salt, pepper, peas, corn and carrots. Cook for 3 minutes, stirring occasionally.
  • Whisk the slurry again (cornstarch settle to the bottom quickly) and add to the skillet. Bring to a boil and cook until filling bubbles and thickens. Add cooked chicken and stir to combine. Turn off heat.
  • Transfer filling to prepared baking dish and flatten with a spatula.
  • Drop spoonfuls of quinoa mixture on top and spread with a spatula to cover the filling evenly.
  • Bake uncovered for 25 minutes.
  • Remove from the oven, let cool for 5 – 10 minutes and cut into 8 squares. Serve hot.

Store: Refrigerate in an airtight container for up to 3 days. 

    Freeze: Leftovers can be frozen for up to 3 months. 

      Make Ahead and Freeze: Assemble, tightly wrap with plastic and then foil, and freeze for up to 3 months. Thaw in the fridge overnight and bake as per instructions + 15 minutes.


        • Cooked chicken breast: Any cooked, grilled or rotisserie cubed chicken works. I usually use Instant Pot chicken breast. If using rotisserie or store-bought chicken, add less salt to the filling.
        • Cooked quinoa: Usually 1 cup of dry quinoa yields 3 cups cooked quinoa. Follow package directions. I use Instant Pot quinoa – sorry, mild Instant Pot obsession here.
        • Vegetables: Onion, peas, carrots, corn, celery and mushrooms. I use frozen peas and corn and then add chopped fresh carrot. You can also use mirepoix. I didn’t have mushrooms and celery on hand, that’s why you do not see it in pictures. Filling was a bit too sweet with corn and carrots.
        • Cheese: Mozzarella or cheddar cheese (sorry no need for Parmesan  cheese – photo mistake).
        • Eggs: They act as a binder for crust. Sorry I have not tried an egg replacer.
        • Milk: Whole milk makes the creamiest sauce. Any milk works. 


        Serving: 1slice | Calories: 357kcal | Carbohydrates: 32g | Protein: 34g | Fat: 10g | Saturated Fat: 3g | Cholesterol: 130mg | Sodium: 469mg | Fiber: 6g | Sugar: 7g

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        56 comments on “Healthy Chicken Pot Pie Casserole with Quinoa Crust

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        1. 5 stars
          Wondering if this could be made with ground chicken? If so, what do you think 1lb or 2 lbs? Can’t wait to try this!

        2. Although most online recipes assume people are unable to follow a basic recipe and require the reader to scroll through numerous photos to the end for instructions, this silly thing scatters the photos throughout the instructions so one would need to print numerous pages of photos. That’s a shame because I would have tried this. Oh well. I would suggest including a print friendly version.

        3. I want to make the chicken pot pie recipe but suppose to make things with 10% ( preferably 5%) of sodium. How can I figure out the sodium percentage? Thank you!

          1. I guess easiest way is to Google how much sodium is in 1 tsp of salt, then calculate amount for 1.25 tsp and deduct it from recipe and divide by # of servings and take total amount of salt % of other ingredients. Or use some calorie calculator online and play around with ingredients with salt.

        4. 5 stars
          Was fascinated with recipe. Looks good and tastes so lovely. thank you for all low carb recipes, Recently diagnosed with T2 diabetes after being”pre” for several years. Have dropped weight and will continue to do so using your low carb recipes. Many thanks, Glenys

        5. 5 stars
          Everyone loved it. I substituted potatoes for the chicken as I was feeding a vegetarian and it was simply delicious. I loved this recipe because I would never go to the effort of making the pastry but it still gives the comfort food feeling.

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