If the thing is useful for a purpose, write This box might come in handy, or can come in handy; UK writers also say come in useful. The idiom often appears with might or on its own.
If someone may enter, write You can come in now. At the door in direct speech, the natural wording is the invitation Come in!; You can come in suits narration instead.
If the usefulness is still ahead of you, write can come in handy: Keep that receipt, it can come in handy if you need a refund. The idiom means the thing will be useful for a purpose; UK writers often say come in useful with the same meaning, so that box can come in useful too is fine.
When the usefulness has already happened, switch to came in handy: The torch came in handy when the lights went out. It also flexes as comes in handy for things that help regularly: That advice comes in handy at work.
If someone is asking or giving permission to enter, write can come in about the person walking in: You can come in now, the doctor is ready. It works for arrivals too: The guests can come in through the side door.
At the door in direct speech, the natural wording is the plain invitation Come in! when someone knocks. Save You can come in for narration or explanation, as in The nurse said you can come in whenever you are ready.
You would say A spare charger can come in handy when you mean it is useful, but You can come in and wait here when you mean someone may enter. Same words, different job.
Quick boundary check: if the subject is a thing doing the helping, use the come in handy form; if the subject is a person and the movement is real, use the entering sense. An umbrella can come in handy describes usefulness; you can come in describes permission to walk in.