Preheat the oven to 400°F and line a baking sheet with parchment paper.
Halve acorn squash and use a spoon to remove seeds and guts.
Rub flesh and skin of acorn squash with 1 tablespoon olive oil. Season with salt and pepper. Place onto prepared baking sheet, cut side down, and bake in the oven until fork tender, 45 minutes.
Meanwhile, heat remaining 2 tablespoons of olive oil in a large, heavy bottomed pot over medium heat. Add the onions and carrots and cook until soft and translucent, 5 minutes. Add garlic, apple and spices. Continue to cook until apples are slightly tender, 8-10 minutes. Season to taste with salt and pepper. Once the squash is cool enough to handle, scoop the cooked flesh into the pot and discard the skin. Add the vegetable broth then bring to a simmer. Cook until apples are softened, 5 minutes.
Turn off the heat and slowly add yogurt while mixing, then use an immersion blender to puree the soup. Season to taste with salt and pepper and serve immediately with more yogurt, toasted seeds and fresh cilantro.
Storage: Leftovers will keep well in the fridge in an airtight container for up to 5 days.