Preheat your oven to 375F. Peel the chayote squash, remove the seeds, and dice into small apple-sized chunks.
Melt 2 tbsp butter in a large skillet over medium heat. Add the diced chayote and cook for 8 to 10 minutes, stirring occasionally, until the pieces are tender but still hold their shape.
Add the granulated erythritol, apple extract, cinnamon, nutmeg, lemon juice, and xanthan gum. Stir well and cook for another 2 minutes until everything is evenly coated and the liquid thickens slightly.
Transfer the filling to an 8x8-inch baking dish and spread it out evenly.
Make the crisp topping by combining the almond flour, chopped pecans, granulated erythritol, cinnamon, and a pinch of salt in a bowl. Add the cold cubed butter and work it in with your fingers or a fork until the mixture forms clumpy, crumbly pieces.
Scatter the topping evenly over the filling, leaving some gaps so steam can escape.
Bake for 22 to 25 minutes until the topping is golden brown and the filling is bubbling around the edges. Let it cool for 10 minutes before serving. Serve warm with a dollop of whipped cream or a scoop of keto vanilla ice cream.