Mexican Lasagna Bowls
Published June 18, 2025 • Updated March 10, 2026
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This is what happens when enchiladas and lasagna bowls meet in a meal prep container. Instead of building one big casserole that I have to slice and hope holds together, I layer everything into individual oven-safe containers so each one is its own ready-to-go meal. You get all the saucy, cheesy comfort of a Tex-Mex casserole, just portioned out and stackable in your fridge or freezer. Grab one, heat it, done.
Each bowl starts with a low-carb tortilla pressed into the bottom of a 2-cup container. Then I go: enchilada sauce, black soy beans, diced green chiles, shredded chicken, more sauce, cheese, another tortilla, and more cheese on top. I use black soy beans instead of regular because they hold their texture through day four in the sauce. Regular black beans get soft and mushy by day two, but these stay firm, and that matters when you’re eating the bowls days after assembly. The whole stack compresses as it bakes, and the tortillas absorb just enough sauce to soften without falling apart.
I tested this with less enchilada sauce once, just to see what would happen. The whole thing tasted flat. The full cup of sauce is non-negotiable. It’s what makes the layers meld together and gives you that rich, saucy bite in every spoonful. If anything, I’d add more rather than less.
What I like about the bowl format over a traditional casserole is the built-in portion control. I’m not eyeballing slices from a 9×13 pan and pretending they’re even. Each container is 45g of protein and 7.5g net carbs, and I know that before I open the lid. I press the layers down with the back of a spoon after assembly to get more surface contact with the container walls. That’s how you get the crispy tortilla edges after baking.
These hold up in the fridge for 4-5 days without getting soggy. The tortillas actually do better than pasta here because they don’t waterlog the way noodles do. Day three is still solid. I freeze a batch every time I make these, and they reheat from frozen without any texture issues. For weekly keto meal prep, these rotate in with my taco casserole and chicken casserole as the three I never skip.
Top them however you want when serving. I usually go with sour cream and sliced avocado, sometimes jalapeños for heat. You can also swap in salsa chicken as the protein if you want a different flavor profile from plain shredded chicken. These bowls handle extras well.
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Ingredients
12 low-carb tortillas, 4-inch -
1 cup red enchilada sauce, divided
-
1 cup black soy beans, drained & divided
-
1/4 cup diced green chiles, divided
-
12 oz cooked, shredded or diced chicken
-
8 oz shredded cheddar cheese
-
2 cup meal prep containers
Step by Step Instructions
Step by Step Instructions
Cut tortillas if necessary
If you’re using 4-inch tortillas, they should fit inside the 2 cup meal prep containers. If you have larger tortillas, you’ll need to cut them to fit your containers. Lay down one tortilla inside each bowl.
- 4 tortillas
Layer the taco lasagna
To each bowl, add the following layers in this order: 2 tablespoons enchilada sauce, 1 tortilla, 1/4 cup black soy beans, 1 tablespoon diced green chiles, 4 oz chicken, 2 tablespoons enchilada sauce, 1 oz shredded cheddar cheese (about 1/4 cup), 1 tortilla, and 1 oz shredded cheddar cheese.
- 2 tablespoons enchilada sauce
- 1 tortilla
- 1/4 cup black soy beans
- 1 tablespoon diced green chiles
- 4 oz cooked chicken
- 2 tablespoons enchilada sauce
- 1 oz shredded cheddar cheese (about 1/4 cup)
- 1 tortilla
- 1 oz shredded cheddar cheese
Bake or store
If enjoying now, place the bowls on a rimmed baking sheet and bake at 350°F for 30 minutes or until the cheese is bubbly and starts to turn golden. Or place in the air fryer, and bake at 350°F for 10–15 minutes. Or microwave for 3-5 minutes. To store in the refrigerator or freezer, cover with lid and place in the refrigerator for up to 5 days or freezer for 2-3 months.
Nutrition disclaimer
The nutrition information provided is an estimate and is for informational purposes only. I am a Doctor of Pharmacy (Pharm.D.); however, this content is not intended to be a substitute for professional medical advice, diagnosis, or treatment. Always consult your physician or other qualified health provider before making any lifestyle changes or beginning a new nutrition program.
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Get My Macros + Recipes →Frequently Asked Questions
Can I make this in a regular casserole dish instead of individual bowls?
I've done it both ways. A 9x13 baking dish works if you're feeding a group. Just layer the same way you would the individual containers and bake at 350 degrees F for about 35-40 minutes. The reason I prefer the bowls is portion control and storage. With a casserole, I'm cutting uneven slices and trying to fit them into containers after the fact. With bowls, I know exactly what I'm grabbing from the fridge each time.
Can I use green enchilada sauce instead of red?
I usually stick with red, but I've tried green and it genuinely tastes like a different dish. Brighter, lighter, less smoky. One of my readers switched to green on his second batch and said the same thing. You can also mix red and green between layers if you want the best of both.
Can I freeze these bowls?
I freeze them every single time I make a batch. Assemble, cover tightly, and they'll keep for 2-3 months. When I'm ready to eat one, I either thaw it overnight in the fridge or bake it straight from frozen. Just add 15-20 minutes to the cook time and keep it covered with foil for the first half so the cheese doesn't get too dark before the center heats through.
Which low-carb tortilla brand works best in these containers?
I've used a few different brands, but Siete grain-free 4-inch tortillas are the easiest. They drop straight into 2-cup containers without any trimming. If you're using larger tortillas, just cut them down to fit. Almond flour and egg white tortillas both hold up well in the layers after a few days in the fridge.
How do I prevent the top cheese from over-browning?
Mine usually start browning around the 20-minute mark. I pull them when the cheese is bubbly and just starting to turn golden, not dark. If yours are getting too brown before the inside is hot, cover with a piece of foil for the first 20 minutes and uncover for the last 10. That keeps the cheese from going past golden while everything heats through.
Can I use ground beef instead of chicken?
I've made these with ground beef and they're good. Brown the beef with some taco seasoning first, drain the fat, then layer it the same way. The bowls come out a little heavier, but the flavor is great if you want a more classic Tex-Mex feel. My keto hamburger helper is another solid ground beef option if you're looking for more meal ideas.
What are black soy beans and where can I find them?
They look like regular black beans but have way fewer carbs and more protein. I use them in these bowls because they hold up in sauce for days without getting mushy, which regular black beans can't do. By day four in the fridge, these still have actual texture. You can find them canned online or in the health food aisle of some grocery stores. Eden Foods is the brand I buy most often.
Used a rotisserie chicken and had these assembled in under 10 minutes flat. Doubled the green chiles because I like heat, and they held up great even after four days in the fridge (layers stayed totally intact, which I did not expect).
Rotisserie chicken is basically how I make these now. The black soy beans are what keep the layers together that long - regular black beans would be mush by day 2.
These are SO good as meal prep, I was genuinely impressed with how well the layers hold up after a few days in the fridge. My one note: the enchilada sauce felt a little light, I ended up spooning extra over mine before eating. But the black soy beans are a great call (you barely notice them), and the macros for how filling this is are kind of wild. Four stars but easily five with more sauce.
The sauce is the one thing I tell people to adjust freely. I go heavier on the bottom layer and usually end up closer to 1.5 cups total. Easy fix once you know where you land.
My son normally has opinions about anything that's 'not real Mexican food', so I wasn't expecting much. He watched me layer the tortillas and enchilada sauce, pulled up a chair, and didn't say another word until his bowl was empty. Making double next time.
That chair pull is the tell. Once he sat down to watch the layers go in, you had him. Double batch is the right call.
Made these for meal prep last week and they were great day one, but by day three the tortillas were completely soggy. Is that just inevitable, or does toasting them first actually help? Wondering if less sauce on the bottom would make a difference too.
Toasting first helps a lot. Dry pan, about 60 seconds per side before you layer. Day 3 holds up way better with that step. Less sauce on the bottom is worth trying too but the toast is the bigger fix.
Brought a batch to a Sunday gathering and people kept asking what was in the layers before they even opened one.
Ha, the layers peek through the container sides. People can't just grab one without asking first.
Brought these to a neighborhood cookout two weeks ago, made them in the individual containers exactly like the recipe shows. My friend who tracks everything grabbed two and immediately started asking what was in them, not because anything seemed off, just because the protein number I mentioned broke his brain. Nobody questioned the tortillas or the beans, the layers just read as the filling. I was honestly nervous about transporting them but they held up with zero mess and the enchilada sauce didn't make anything soggy. Making these for every cookout this spring, probably doubling the batch because four servings disappeared before I even got one.
Four servings gone before you got one. The black soy beans are the reason the protein number looks unreal, nobody expects them in something that eats like comfort food.
Mexican food was the one thing I kept grieving when I went keto eight months ago. Not bread, not pasta, this. So I almost skipped this recipe, figured it would just remind me of what I'd given up. Made it Sunday for meal prep, sat down with the first bowl, and had to stop for a second. The enchilada sauce soaks into the tortilla layers and gets this depth I wasn't expecting from something you just assemble in containers and throw in the oven. I've been pulling these out of the fridge all week actually looking forward to lunch, which has not been my experience with meal prep ever. Making a double batch this weekend and trying green enchilada sauce to see what that does.
Green changes it completely. Brighter, way less smoky, almost feels like a separate recipe. The reader who first switched to green said he couldn't go back to red, so fair warning.
I made peace with the idea months ago that real Mexican food was just gone on keto. Then I made these last Sunday, layered in the enchilada sauce and chicken, took one bite and just stopped. That is the flavor. The one I have been missing since I started this whole thing. So grateful this recipe exists.
First time making these and I kept second-guessing the layering order, but once they came out of the oven I understood. The tortillas held their shape way better than I expected, no soft spots anywhere. Do you think ground beef would work here instead of shredded chicken? I have some I need to use up this week.
Went in skeptical about the tortilla layers holding up by day three, but they stay intact SO much better than the grain-free wraps I've been using. Everything else on my Sunday prep rotation is suddenly on notice.
They firm up as the enchilada sauce soaks in overnight. Day 3 is my favorite batch.
Tried green enchilada sauce instead of red and added sliced jalapeños between each tortilla layer. The tomatillo tang cuts through all that cheese differently than red does (less heavy, brighter), and the jalapeño heat stacks through the layers. You don't really feel it until you're a few bites in. One thing I figured out: let the bowls sit 10 minutes before they go in the oven. The tortillas soak up the sauce and the whole thing holds together when you cut in.
That pre-oven rest makes so much sense. Tortillas go in pretty dry without it. And jalapeños through every layer instead of just on top changes when the heat actually hits.
Made these Sunday for meal prep and my husband, who gives every keto recipe a full smell test before committing, grabbed one straight from the fridge cold and ate it standing over the sink. Didn't even ask to heat it up. That's how I knew. The enchilada sauce soaks into the tortillas overnight and somehow makes them better than fresh out of the oven. Doubling the batch next Sunday.
The sink test wins every time. My husband's version is grabbing it straight out of the container before I can even plate it.
Forgot meals like this were still on the table. Enchilada sauce doesn't disappoint, though next time I'd push the spice more.
Stir a pinch of cayenne into the enchilada sauce before layering. The green chiles are pretty mild so they won't carry the heat on their own.
Most keto Mexican casseroles I've made turn into a pile when you try to portion them out. Layering in individual containers was the fix I didn't know I needed. Better protein ratio than anything else in my lunch rotation right now.
Most of that protein is the chicken + soy beans together. Regular black beans won't make it past day 2 in a container.
Switched to green enchilada sauce on my second batch and it genuinely tastes like a different dish. Brighter, less heavy. Didn't expect that from something baked in a container. Also noticed the tortillas on the bottom layer get almost pasta-like after a night in the fridge (absorbs the sauce, softens just right), and honestly I liked it more than the fresh version. If you're using Siete grain-free 4-inch tortillas, they drop straight into the 2-cup containers without any trimming. Running these through my Sunday meal prep now, and the 44g protein per serving is what keeps them there, but they also reheat cleaner than anything else I've put in these containers.
Yeah the overnight version is better. Tortillas absorb into the sauce and compress and it almost slices cleaner than fresh out of the oven. Should've noted that.