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!

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.

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!

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.

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.

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.

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.

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.

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.

Top with Shredded Cheese

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

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.

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.

Recipe FAQs

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More quinoa recipes: 

• This easy quinoa salad is tossed in a homemade lemon dressing and it’s so light and fresh and delicious!
• Nothing screams summer like this balsamic caprese quinoa salad. 
• This Asian quinoa salad is perfect to bring to a BBQ or potluck, it’s delicious and feeds a crowd. 
• I make this roasted vegetable honey mustard quinoa salad on repeat!

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