Both the Eastern Orthodox and the Roman Catholic Church would consider themselves the one true church and they can't both be right.
There are also so many protestant denominations.
My question is this - how do we discern the truth?
We can discern the truth in a few ways. It is best, though, to start with a source that all churches and denominations agree on: the Gospel according to Matthew.
Now when Jesus came into the district of Caesarea Philippi, He was asking His disciples, “Who do people say that the Son of Man is?” And they said, “Some say John the Baptist; and others, Elijah; but still others, Jeremiah, or one of the prophets.” He said to them, “But who do you say that I am?” Simon Peter answered, “You are the Christ, the Son of the living God.” And Jesus said to him, “Blessed are you, Simon Barjona, because flesh and blood did not reveal this to you, but My Father who is in heaven. “I also say to you that you are Peter, and upon this rock I will build My church; and the gates of Hades will not overpower it. (Matthew 16:13-18)
According to Jesus, the gates of Hades will not overpower the Church. So, anyone who teaches that they
did overpower the Church, even if only temporarily, cannot be right. This means that we can rule out any denomination that claims a discontinuous history of the Church, where the true faith was lost and then rediscovered, the "restorationist" denominations.
I would further argue that this criterion effectively rules out most non-restorationist Protestant denominations too; as Martin Luther wrote against the Anabaptists, infant baptism was the universal practice for a thousand years before the Protestant Reformation. If infant baptism were not really baptism at all, then for over a thousand years there were no true baptisms, and therefore no Church. The same criticism applies to any denomination that teaches something contrary to what was universally accepted in the past: the divinity of Jesus Christ and the Holy Ghost, baptismal regeneration, Christ being truly present in the Eucharist, the necessity of having bishops with apostolic succession, the unity of the Church, and so on. Can any Protestant denomination claim that last item? I would say no, not in the way that the Nicene Fathers meant it when they composed the Creed, saying "one holy, catholic and apostolic Church."
Now, there are some interesting edge cases. One would be the "Landmark Baptists," who claim that the various supposedly heretical sects throughout history were actually preserving the characteristic Baptist doctrines from the time of the Apostles, and in this way there is a continuous history of the Church. But even if we grant that (and we shouldn't), there is still the problem of these sects having held beliefs that the Baptists would see as heretical today, from Gnosticism to extremely high sacramentalism. If I remember correctly, the original promoters of Landmarkism argued that these beliefs were falsely attributed to these groups by the Catholic Church, but there is simply no evidence that this is the case, and if you can make up facts about history with no evidence, there is no chance for rational discussion.
Similarly, many Protestants will claim that there were always some local churches or individual believers who held the true faith, even when the institutional Church accepted errors. But again, there is no evidence for these secret sola-scriptura-believing Protestants; it's just an assertion with no evidence. And again, if that's allowed, then no productive discussion can be had.
To put it bluntly, I think this rules out all of Protestantism. There's much more that could be said about the differences between the apostolic churches, and if anyone's interested in hearing my thoughts I'd be happy to continue, but this post is already very long, so I'll leave it at that for now.