Not always the same. Compare some situations:

1. Someone is waiting for you outside near your home. He just wants to have a talk with you. And he does not ask for a permission to enter. But you decide to invite him since you prefer to talk at your home. Then you call: Зайдите! or Зайдите на минуту!

2. Someone is standing behind your door waiting for a permission to enter. You asked him to wait for a couple of minutes since you were busy. Finally, you say: Заходите! or Входите!

3. An unexpected visitor comes to you suddenly. Then you can say: Войдите! or Входите! And "войдите" fits better.