Cut the squash in half and remove the seeds. Cut the bell peppers in half and remove the core, membranes and seeds. Peel the garlic cloves but keep them whole.
Sprinkle a tiny little bit of salt and pepper over the open side of the squash and bell peppers and place them all face down in a large baking dish.
Add garlic cloves and water and place in the oven. Cook uncovered for about 30 minutes, until the squash and peppers are fork tender and the garlic turns nice and golden brown.
Remove vegetables from the oven and let them cool for little while.
Meanwhile, chop the onion and add it to a large saucepan. Cook over medium heat until fragrant and slightly brown, about 5 minutes.
Add cumin, cinnamon, nutmeg, salt and pepper and continue cooking for about one minute.
Remove as much skin as you can from the bell peppers, chop them coarsely and add them to the pot. Scoop out the flesh of the roasted squash and add that to the pot as well.
Throw in the garlic and water, bring to a boil then lower the heat and simmer for about 5 minutes.
Remove from heat and reduce to a smooth puree with the help of a handheld blender.
Pass soup through a fine mesh strainer. You might want to help it through by swirling it around with a laddle (this step is optional but will make your soup extra creamy and velvety, so I think it's really worth it. It does change the texture dramatically.)
Return soup to saucepan and bring back to a simmer, then kill the heat.
In a small bowl, mix the coconut cream and Greek yogurt together and incorporate that to the soup using your handheld blender (using the blender as opposed to a simple whisk will prevent the yogurt from curdling and will make your soup really silky.)
Transfer to serving bowls and garnish as desired.
Notes
*I made my whole grain croutons simply by cutting thick slices of whole grain bread into cubes and toasting them slightly in a non stick pan. I also roasted a few extra cloves of garlic to use as garnish and mixed a couple of tablespoons of Greek yogurt and coconut cream together, which I then placed in a small squeeze bottle to make a pretty design.