Cook the whole wheat noodles according to package instructions until al dente. Drain and set aside.
Heat olive oil in a large skillet over medium-high heat.
Add diced onion and minced garlic to the skillet and sauté for 2-3 minutes until fragrant and translucent.
Add the lean ground beef to the skillet and cook, breaking it apart with a spatula, until browned and cooked through, about 6-8 minutes.
Add broccoli florets, sliced bell peppers, and shredded carrots to the skillet. Cook for 4-5 minutes until vegetables are tender-crisp.
Stir in the grated fresh ginger, low sodium soy sauce, oyster sauce, black pepper, and crushed red pepper flakes. Mix well to combine all ingredients.
Add the cooked whole wheat noodles to the skillet and toss everything together until the noodles are evenly coated with the sauce and heated through, about 2 minutes.
Remove from heat and garnish with thinly sliced green onions and toasted sesame seeds.
Serve immediately.