The early church fathers are unanimous in claiming that Peter died in Rome, by crucifixion, during the persecution of Nero in AD 64. As for crucifixion upside down, that is also testified to, but the evidence is weaker for this particular form of crucifixion. The apocryphal Acts of Peter is the earliest reference to crucifixion of Peter upside down. The earliest reference to the martyrdom of Peter comes from the letter of Clement of Rome (about AD 90). He said, in his Letter to the Corinthians, "Let us take the noble examples of our own generation. Through jealousy and envy the greatest and most just pillars of the Church were persecuted, and came even unto death… Peter, through unjust envy, endured not one or two but many labours, and at last, having delivered his testimony, departed unto the place of glory due to him." Not much there as to the means or location of his death, but that it was an execution is clearly implied. Ignatius, in his Letter to the Romans about AD 110 claimed that Peter was bishop of Rome. Irenaeus of Lyon, about AD 180, agrees that Peter served in Rome. Tertullian, about AD 195 declared "But if you are near Italy, you have Rome, where authority is at hand for us too. What a happy church that is, on which the apostles poured out their whole doctrine with their blood; where Peter had a passion like that of the Lord, where Paul was crowned with the death of John (the Baptist, ie. by being beheaded). Dionysius of Corinth, also about AD 200 "You (Pope Soter) have also, by your very admonition, brought together the planting that was made by Peter and Paul at Rome and at Corinth; for both of them alike planted in our Corinth and taught us; and both alike, teaching similarly in Italy, suffered martyrdom at the same time" When Eusebius reported the crucifixion of Peter and the beheading of Paul in Ecclestiacial History, he was simply passing along a tradition which has been the unanimous opinion of the church for two hundred years.
Tradition has that Peter’s body is contained in a crypt below St. Peter’s Basilica in Rome. This is actually not all that far-fetched a claim. In fact, when the sarcophygous claimed to contain his body was studied in the 1960’s (Margherita Guarducci, 1963-1968) the evidence supported that it was of a man about 60 years old who died in the first century AD. I certainly would not base my faith on this being his body, and besides, it is not clear the significance to a Christian to have the actual remains of Peter.
In conclusion, we can reasonably conclude that Peter was in fact crucified in Rome. As for his crucifixion upside down, this is much more weakly attested to in only one ancient source which is probably much less reliable that Clement, Ignatius, Irenaeus, Tertullian, Eusebius and many others.
https://evidenceforchristianity.org/what-is-the-evidence-that-peter-was-crucified-upside-down-in-rome/
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