Baked Quinoa Casserole

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This Baked Quinoa Casserole is an easy, hearty main dish that is perfect for fall. It’s ready in under 30 minutes and is a great gluten-free dinner recipe to feed a crowd! Even my kids love this cheesy quinoa recipe loaded with sausage, apples and veggies!

overhead view of baked quinoa casserole in a cast iron pan with a spoon taking a scoop out of it


What better way to welcome fall than with a cheesy Baked Quinoa Casserole? It’s a healthy-yet-comforting dish that feeds a crowd. Plus, it’s ready in 30 minutes and is loaded with delicious fall flavors including apples and veggies.

This Baked Quinoa Casserole is the perfect dish for entertaining in the fall. Whether you bring it to a potluck, book club or serve it while you watch the big game, it’s a healthy and flavorful meal everyone loves.

What I love about this Baked Quinoa Casserole is that it satisfies the health-conscious while being hearty enough for people who prefer more substantial meals. Plus it’s gluten-free so it can be served when you’re entertaining people with food allergies.

front view of a fork lifting a bite of Baked Quinoa Casserole out of a bowl showing a stringy cheese pull topped with fresh parsley

Baked Quinoa Casserole Recipe: Ingredients and Substitutions

Let’s chat about the ingredients in this quinoa casserole recipe, as well as some possible substitutions.

  • Quinoa. Obviously quinoa is one of the main ingredients in this recipe. So I don’t recommend substituting it. However, an equal amount of cooked brown, rice or wild rice can be used in its place.
  • Smoked Sausage. Use your favorite sausage variety in this recipe with great results: chicken sausage, Italian sausage, etc.
  • Green Peppers. Use any color bell pepper, omit them or substitute a different vegetable such as carrots, celery, more onion, etc. etc.
  • Apple. I used Pink Lady apples in this recipe for their slightly sweet, slightly tart flavor and firm texture. Use your favorite apple variety.
  • Fire Roasted Tomatoes. Again, I tested this recipe once with plain diced tomatoes and once with fire roasted, and I just prefer the flavor of the fire roasted better. It’s totally up to you and you can use any flavor/variety of canned diced tomatoes that you wish, as long as you are aware that the flavor of tomatoes will change the overall flavor of the dish.
  • Whole Milk. 2%, cream or half and half are good substitutes for whole milk.
  • Sharp Cheddar Cheese. The sharper the better!
overhead view of the ingredients in this Baked Quinoa Casserole recipe on a wood cutting board

How to Cook Quinoa Perfectly

Ok, I feel the need to discuss how to actually cook quinoa before I proceed any further with this baked quinoa recipe. Because I have lots of quinoa recipes on my site, like this Asian quinoa salad, roasted vegetable quinoa and this caprese quinoa salad.

Quinoa is really easy and quick to make, however it is also very easy to mess up. There is a fine line between perfectly fluffy quinoa and a chewy yet mushy mess that is totally inedible. So here are a few tips on how to cook quinoa perfectly every time.

  1. Rinse the quinoa. This removes the saponins on the outside of the quinoa, which are a naturally occurring chemical that give un-rinsed quinoa a bitter taste. Use a fine metal strainer to rinse the quinoa before cooking to prevent any bitterness.
  2. Use a 1:2 ratio of quinoa to water. I have seen different packages of quinoa suggest other ratios, but I have found the best results when using 1 part quinoa, 2 parts water.
  3. Boil the water first. Always bring the water to a boil and then add quinoa.
  4. Add quinoa & return to a boil. After the quinoa is added to the boiling water, make sure the water returns to a boil before reducing the heat (see below). This happens very quickly, so be careful to watch it so the water doesn’t boil off.
  5. Reduce heat to a simmer. This is where I have gone wrong in the past. Sometimes, in an attempt to speed up the process, I cook the quinoa with the heat turned up too high. When you do this, the water boils off before the quinoa can fully cook, leaving you with a crunchy mushy mess.
  6. Cook for 15 minutes.  15 minutes is the perfect cooking time for quinoa.
  7. Fluff. After 15 minutes all the water should be absorbed and the quinoa should be soft (not crunchy or hard). Take a fork or a wooden spoon and fluff the quinoa.
  8. Cover and let it rest for 15 minutes. This is another key step in cooking quinoa that is often overlooked. Letting the quinoa cook in the residual heat from the burner (turned off) and in its own steam really finishes the process and results in a perfectly fluffy quinoa every time!

And that’s it! Please let me know in the comments below if you have any other questions about cooking quinoa.

In this quinoa casserole recipe, we cook the quinoa first, and then proceed with the rest of the recipe. This can be done right when you begin cooking, or anytime before.

a bowl of cooked quinoa

How to make Baked Quinoa Casserole

Now that you know how to cook perfect quinoa, let’s jump into how to make this cheesy Baked Quinoa Casserole recipe.

Brown Sausage & Veggies

The first step in this Quinoa Casserole recipe is to brown the sausage and veggies. Start with the sausage alone, and once it just begins to brown add the onion, bell pepper and minced garlic. Cook until everything is nicely browned.

I recommend starting with 1 TBS olive oil and add more if the sausage doesn’t seem to be browning as fast as you’d like it to. In one of the trials of this recipe I added 1/2 TBS more olive oil just to ensure everything got nice and crispy.

Browning the meat and veggies adds an extra depth of flavor to this Baked Quinoa Casserole that really can’t be understated. Please make sure not to skip this step.

Overhead view of sausage, peppers and onions being browned in a cast iron skillet making Baked Quinoa Casserole recipe.

Add the apples, tomatoes and spices. 

Don’t cook the apples.e the apples retain more of their flavor and crunch when they are mixed into the ingredients and not cooked.

overhead view of a cast iron skillet after adding tomatoes and apples to the cooked sausage, peppers and onions in the making of this Baked Quinoa Casserole recipe

Add the Milk and Cheese 

The only note about this step is that you may need to return the pan to your heat source and warm the mixture over medium-low heat to get the cheese to milk. However if you work quickly and use a pan that retains heat (like a cast iron skillet) it should melt right away.

cheese being poured onto the top of the quinoa casserole in a skillet

Add the Cooked Quinoa 

Once the cheese is nicely melted and the mixture is smooth, add the cooked quinoa and stir to combine. At this point there will be no need to cook over the stovetop anymore. The rest of the cooking/melting will be done in the oven.

Overhead view of a cast iron skillet after the cooked quinoa has been added in the making of this Baked Quinoa Casserole recipe

I felt it was important to include the photo below to show the consistency of the final Baked Quinoa Casserole mixture before it’s topped with cheese and baked. Notice that it is wet, but not soupy.

As long as the quinoa is cooked correctly, it will absorb some of the liquid and you will get a mixture that looks like the picture below. Be sure everything is evenly distributed throughout the Baked Quinoa Casserole mixture before adding the cheese to the top.

overhead view of the final quinoa mixture in a cast iron skillet before adding cheese on top in the making of this Baked Quinoa Casserole recipe

Top with Shredded Cheese

Before putting the dish in the oven, top it with a generous serving of cheddar cheese. 

front view of a hand sprinkling shredded cheddar cheese on top of a skillet full of Baked Quinoa Casserole

Bake the Quinoa Casserole

Now it’s time to bake the casserole. Since everything is already pre-cooked on the stovetop, the goal of baking here is to warm the dish all the way through and melt the cheese on top.

I recommend baking this quinoa casserole at 400 degrees F for about 10-15 minutes, util the cheese is melted.

overhead view of Baked Quinoa Casserole in a cast iron skillet after baking, with melted cheese on top sprinkled with fresh parsley

Serve

Once the cheese is melted, remove the Quinoa Casserole from the oven (be careful, it’s heavy), and let it cool for about 5 minutes or serve it right away.

This is an entire meal in one skillet, which I absolutely love. And everyone in my family enjoyed it a little differently. You can serve it with a side salad (like this kale salad) or some homemade no knead bread.

Store

Store leftovers in an airtight container in the refrigerator for up to 5 days.

Freeze

You can freeze the entire casserole before baking (meal prepping for having a baby, giving a meal to a friend, etc.). Just assemble the casserole and then cover it tightly with plastic wrap and foil and freeze. Let it thaw in the refrigerator overnight and then bake according to the recipe instructions.

You can also freeze leftovers in an airtight contianer in the refrigerator for up to 2 months.

up close overhead view of a spoon taking a scoop of Baked Quinoa Casserole out of the cast iron skillet

Recipe FAQs

What to serve with Baked Quinoa Casserole?

Add a sprinkle of fresh parsley. For the adults in your life who don’t mind a few green things on top of their cheese, fresh parsley not only adds a great pop of color but also a nice fresh flavor.
Sour cream. My son enjoyed this Baked Quinoa Casserole with a dollop of sour cream (like most foods he eats…LOL).
Fresh Avocado or Guacamole. I know this isn’t really a Mexican dish, but oh boy a little fresh avocado (mashed or sliced) tastes amazing served with this baked quinoa. My oldest daughter and I swirled some leftover guac into our helpings and absolutely loved it!
Plain. My husband and other two kids (including my 18-month old) dug straight in and politely turned down any add-ins because it’s just that good on it’s own.

Is quinoa healthy?

As far as grains go it is very healthy – boasting 8 g of protein and 5 g of fiber in one serving.

up close overhead view of a spoon taking a scoop of Baked Quinoa Casserole out of the cast iron skillet

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Baked Quinoa Casserole Recipe

Laura
This Baked Quinoa Casserole is an easy, hearty main dish that is perfect for fall. It’s ready in under 30 minutes and is a great gluten-free dinner recipe to feed a crowd! Even my kids loved this cheesy quinoa recipe loaded with sausage, apples and veggies! 
5 from 5 votes
Course Main Course
Cuisine American
Servings 8 Servings
Calories 318.7
Prep Time20 minutes
Cook Time10 minutes
Total Time30 minutes

Ingredients 
 

Instructions 

Cook the Quinoa:

  • Bring 1 ½ cups of water and ¼ tsp salt to a boil.
  • Add quinoa and return to a boil.
  • Once water is boiling turn the heat down to a simmer.
  • Simmer on low for 15 minutes.
  • After 15 minutes turn off the heat, stir the quinoa, and return the lid to the pot.
  • Let the quinoa sit covered for 15 more minutes.
  • After 15 minutes, fluff the quinoa with a spatula and it’s ready to use in this baked quinoa recipe.

Make the Baked Quinoa Casserole:

  • Preheat oven to 400 degrees F
  • Add 1 TBS olive oil to a 10” round cast iron skillet.
  • Add sausage to the skillet and cook until it just starts to brown.
  • Add onion, bell pepper and minced garlic and cook for 5-8 minutes until the onions are translucent.
  • Remove from heat and add apples, stir to combine.
  • Add canned tomatoes, garlic salt, 1 cup cheese and milk and stir until combined and the cheese is melted (you may need to return the pan to the heat source and cook on low heat to get the cheese to melt). 
  • Add cooked quinoa and stir until combined.
  • Top with remaining 1 cup of cheese
  • Bake in preheated oven for 10 minutes or until the cheese is melted.
  • Serve warm with a sprinkle of fresh parsley if desired.

Video

Notes

Ingredient Substitutions
  • Quinoa. Obviously quinoa is one of the main ingredients in this recipe. So I don’t recommend substituting it. However, an equal amount of cooked brown, rice or wild rice can be used in its place.
  • Smoked Sausage. Use your favorite sausage variety in this recipe with great results: chicken sausage, Italian sausage, etc.
  • Green Peppers. Use any color bell pepper, omit them or substitute a different vegetable such as carrots, celery, more onion, etc. etc.
  • Apple. I used Pink Lady apples in this recipe for their slightly sweet, slightly tart flavor and firm texture. Use your favorite apple variety.
  • Fire Roasted Tomatoes. Again, I tested this recipe once with plain diced tomatoes and once with fire roasted, and I just prefer the flavor of the fire roasted better. It’s totally up to you and you can use any flavor/variety of canned diced tomatoes that you wish, as long as you are aware that the flavor of tomatoes will change the overall flavor of the dish.
  • Whole Milk. 2%, cream or half and half are good substitutes for whole milk.
  • Sharp Cheddar Cheese. The sharper the better!

Store

Store leftovers in an airtight container in the refrigerator for up to 5 days.

Freeze

You can freeze the entire casserole before baking (meal prepping for having a baby, giving a meal to a friend, etc.). Just assemble the casserole and then cover it tightly with plastic wrap and foil and freeze. Let it thaw in the refrigerator overnight and then bake according to the recipe instructions.
You can also freeze leftovers in an airtight contianer in the refrigerator for up to 2 months.

Nutrition

Serving: 0.5cup | Calories: 318.7kcal | Carbohydrates: 16.8g | Protein: 17.7g | Fat: 19.2g | Saturated Fat: 9g | Polyunsaturated Fat: 0.3g | Monounsaturated Fat: 1.3g | Cholesterol: 57.9mg | Sodium: 854mg | Potassium: 146mg | Fiber: 2.4g | Sugar: 3.5g | Vitamin A: 370IU | Vitamin C: 21.8mg | Calcium: 227mg | Iron: 2.3mg

Nutrition information is automatically calculated, so should only be used as an approximation.

Did you enjoy this recipe? Have a question? Leave a comment below!

More quinoa recipes: 

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Recipe Rating




14 Comments

  1. 5 stars
    This was super tasty and versatile! I used a chicken apple sausage and added some finely diced broccoli and it was so delicious!

  2. 5 stars
    Thank you Laura, for the step by step instructions. I embellished the recipe to suit my tastes (added some rosemary and oregano + some chopped sun dried tomatoes, olives and chillies to give a bit of a zing. I also used 1/4 cup coconut cream instead of milk and i used a little less cheese – my choice was a light parmesan). I don’t own a pan that can go safely into the oven so transferred it to a loaf pan. Worked great. Served it with sour cream and avocado on the side. It was a total hit! What a perfect quick and amazing meal that you can pretty much prepare in advance. Thank you so much!

  3. I am planning on making this later today. My question is, do you add the liquid of the canned tomatoes or strain it?

  4. Haven’t made this yet. Can you substitute vegetarian sausage for real sausage? Would you get a flavourful casserole? Thanks.

  5. CAN THIS DISH BE MADE IN LARGER PORTIONS AND THEN FROZEN FOR A QUICK MEAL DURING RUSHED HOLIDAY SEASONS.
    I hope you can read this. your other comments, as well as mine, are such a faint gray you can barely make it out. not sure why everything on other sites is fine. can’t wait to try this. I have never eaten Quinona, but my friend is gluten free so I am looking for yummy hearty dishes for them. thank you soo much for the pictures.

    1. Hello Kathleen! I will look into darkening the comment font for you! 🙂 You absolutely can freeze this recipe! I’d recommend freezing it in a baking dish that you can simply remove from the freezer and put in the oven!

  6. I think I need to go get some quinoa, because this looks like COMFORT in a casserole. I want to just dig into that cheesiness. Tillamook cheese is some of the best.