Preheat the oven to 350 degrees F.
Cut the tops off the zucchini and cut lengthwise.
Scrape out the seeds and a small amount of the inside squash. Don't throw away the scraped-out insides. Save them for the filling.
Set aside zucchini boats until ready to stuff.
In a large skillet set over medium-high heat add ground beef.
Cook until browned, draining off the fat if necessary.
Add in chili powder, garlic powder, cumin, oregano, smoked paprika, kosher salt, chipotle chile powder, and water. Stir to combine and cook down until the water is evaporated.
Toss in chipotle pepper, red bell pepper, yellow onion, and zucchini insides. Cook until the vegetables start to soften, about 7 minutes.
Line a large rimmed baking sheet with foil and lay out all six zucchini boats.
Divide the filling by six and spoon it into the zucchini.
Equally, divide cheese and sprinkle it over each zucchini boat.
Bake uncovered for about 30 minutes. If your zucchini is very large it may take a little longer to bake.