Slice the flank steak against the grain into very thin strips to ensure maximum tenderness.
In a small bowl, whisk together the chili powder, ground cumin, smoked paprika, sea salt, black pepper, and lime juice to create a concentrated marinade.
Toss the steak strips in the marinade until evenly coated and let them sit for 5 minutes to absorb the flavors.
Heat half of the olive oil in a large non-stick skillet over medium-high heat.
Add the sliced red bell peppers and red onions to the skillet, sautéing until they are tender and slightly charred, then remove them from the pan.
Add the remaining olive oil to the same skillet and sear the steak strips for 2-3 minutes until they are browned and fully cooked.
Wipe the skillet clean and place the whole grain tortilla inside over medium heat.
Sprinkle half of the Monterey Jack cheese over one half of the tortilla, then layer on the cooked steak and sautéed vegetables.
Top with the remaining cheese and fold the tortilla in half to cover the filling.
Cook for 2 minutes per side until the tortilla is golden brown and the cheese is completely melted.
Slice the quesadilla into wedges and serve immediately while hot.