Preheat oven to 400 degrees. Line a baking sheet with parchment paper. Add brussels sprouts, butternut squash and apples to the baking sheet then toss in melted ghee. Top with dried thyme and rosemary along with a couple pinches of salt. Place in the oven to bake for 40 minutes, tossing every 10 minutes to help cook evenly.
After 40 minutes, add pecans and cranberries and cook for another 10 minutes.
In a bowl, whisk together maple syrup, olive oil, lemon zest and juice then pour over the veggies and toss to coat. Top with flake salt and black pepper before serving.