This is a good question.
Unfortunately, many people think church is just plural for Christians. This is not the case.
I think there are two errors which must be avoided when talking about "what makes a church a church":
I think the best approach is to understand the church as "God's worshiping assembly". We see this as early as Genesis 4:26 when "at that time the men began to call on the name of YHWH". This small group of men turns into an entire people Exodus 7:16, "Let my people go, so that they may worship me in the wilderness." This idea is carried all the way up through the New Testament:
In 1 Corinthians 11:18, we read of instructions for “when you come together as a church,” indicating that there was a unique gathering “as a church” that was not the same as a few Christians hanging out and talking about Jesus. Hebrews 10:25 commands us not to neglect meeting together (literally, “do not forsake the assembly of yourselves”). The word for “meet together,” episynagogen, refers to the formal gathering of God’s people for worship, not just friends listening to sermon downloads in the same room or engaged in an inductive bible study. [Source]
Following Berkhov and Kuyper after him, the church is 100% organism and 100% institution. The Bible never chooses between these two. It is both "body" and "temple". I could go on, but if you are interested in reading all about the Biblical Theology of the Church, please see Ed Clowney's article here.