Plan, build, upgrade, and adjust your village.

It is great to have storage and production buildings but they are no good if they get destroyed every night!

Make sure you have a strong defensive layout that keeps zombies away from your vital buildings.
Always repair and upgrade your defenses. Should you notice that zombies always break through at one side or always destroy the same buildings, change the layout of your village and improve your defenses.

Most villages evolve over time and you will have to find the right answer to new zombie threats.