There is a debate as to whether or not Jesus was talking about individual conversion or church-wide conversion when He spoke to Nicodemus in John 3.
But it isn't an either-or. It is a both-and.
"Unless a man is born again, he cannot see the kingdom (John 3:3, 5). But then Jesus tells Nicodemus that "you all" must be born again (John 3:7), and He consistently uses the plural in His explanation to Nicodemus. Nicodemus was an individual who needed to be born again, but he was also a representative of all Israel. The whole nation needed regeneration, and that is what happened at Pentecost. The valley of dry bones came to life. So did the Nicodemus bones." - Wilson, AC, p48.