Fill a large bowl halfway with water. Add lemon juice and mix. Peel, core, and slice apples and pears, putting them in the lemon water to prevent browning.
Drain fruit; do not rinse. Place drained fruit, 1/4 cup water, and cinnamon stick in a multi-functional electric pressure cooker (such as Instant Pot®). Set the Manual mode to high pressure according to manufacturer's instructions; set timer for 3 minutes. Allow 10 to 15 minutes for pressure to build.
Release pressure using the natural-release method according to manufacturer's instructions, up to 15 minutes. Unlock lid. Remove and discard cinnamon stick. Pass the cooked fruit through a food mill; sauce will be slightly coarse. Blend fruit with an immersion blender for a smoother sauce.