Minecraft wiki entry for Shelters, associated text: Build a fence around your house to keep unwanted mobs out. This includes houses on islands, as drowned can still attack from the water.
Dig your own mine under your house, accessible through a stairway or a ladder. This provides a safer, more controlled alternative to finding things through a dark cave where mobs can spawn, though it requires more work and resources since the entire mine must be dug by the player.
Use different chests for different things to avoid confusion and provide a sense of greater space. For example, one chest can be for stone, another chest can be for deepslate, andesite, granite, and diorite, another chest can be for spare tools and armor, so on, so forth.
Use barrels instead of chests when possible. Barrels do not require a free space above, take up less space, and look rather unique, but they cannot be doubled for greater space like chests can.