Heat the oven to 425 degrees. Peel the squash, then cut it in half. Remove the seeds and pulp from each side. Cut the squash into cubes. Line 1-2 baking sheets with a silicone mat or parchment paper, put the squash on the sheets and put in the oven for about 30 minutes, or until soft and starting to brown.
You can also roast the squash before cutting it into cubes, by putting each half face down on the baking sheets. Once roasted, you can cut it into cubes then.
While the squash is roasting, chop the apple into cubes. Then, chop the onion, garlic and ginger.
Once the squash is done cooking, heat a large soup pot or stock pot on medium-low heat. Once hot, add the oil then add the garlic and ginger and cook until fragrant, about a minute. Add the onion and a pinch of salt and cook until the onion is starting to brown or caramelize.
Add the chopped squash and apple to the soup pot. Add in all spices except the chili flakes and pepper and stir well. Next, add in your vegetable broth. The broth should be about 1 inch above the squash and apple mixture. Bring to a boil.
Once the soup is boiling, simmer until the apples are soft.
Once the apples are soft, add the soup to a blender or use an immersion blender to blend all of the ingredients well until they are smooth. You can blend it as much as you want, depending on if you want it a little grainy or very smooth.
If you poured the soup into a blender, pour it back into the soup pot. Stir well, add the chili flakes and pepper and check for taste. Add more salt if needed. The soup is ready to serve. Top with the pepitas or pumpkin seeds, croutons or any other toppings you like. Enjoy!