Heat olive oil in a large Dutch oven or soup pot over medium-high heat. Once shimmering, add diced onion and cook for 3-4 minutes until translucent, stirring occasionally.
Add minced garlic to the pot and stir constantly for 1 minute until fragrant. This prevents the garlic from burning while releasing its aromatic oils into the oil base.
Add cubed butternut squash and peeled apple chunks to the pot, stirring to coat everything with the oil mixture. Cook for 2-3 minutes to lightly caramelize the edges of the vegetables.
Pour in vegetable broth and bring the mixture to a boil over high heat. Once boiling, reduce heat to medium and simmer for 15-18 minutes until butternut squash is fork-tender and falling apart easily.
Stir in ground sage, nutmeg, cayenne pepper, salt, and pepper into the apple butternut squash soup recipe. Add fresh thyme leaves and maple syrup, stirring well to combine all seasonings throughout the pot.
Remove from heat and carefully transfer the soup to a blender in batches, or use an immersion blender directly in the pot. Blend until completely smooth, working in stages if needed to avoid overflow.
Return blended soup to the pot over low heat and stir in heavy cream slowly. Heat for 2-3 minutes without boiling to warm through completely and let flavors meld together beautifully.
Taste and adjust seasonings as needed before serving hot in bowls garnished with fresh thyme sprigs.