Q. Do we know that Paul was imprisoned a second time in Rome and was martyred under Nero? If so, how do we know?
A. There is nothing definitive since we have to rely on history and tradition rather than an inspired account from the Bible. There is the implication of the matter found in 2 Timothy 4, but the details we have often been taught – that Paul was executed under Nero after a second imprisonment in Rome – are a matter of early Christian writings that have been passed down.
One of the earliest, if not the earliest, references to Paul as a martyr, is in the letter called I Clement. Clement’s writing (often dated around AD 96) says Peter and Paul were martyred, and says Paul’s martyrdom occurred in or after he had been to “the extreme limit of the west” (Rome? Spain?).
But not to dwell upon ancient examples, let us come to the most recent spiritual heroes. Let us take the noble examples furnished in our own generation. Through envy and jealousy, the greatest and most righteous pillars [of the Church] have been persecuted and put to death. Let us set before our eyes the illustrious apostles. Peter, through unrighteous envy, endured not one or two, but numerous labours, and when he had finally suffered martyrdom, departed to the place of glory due to him. Owing to envy, Paul also obtained the reward of patient endurance, after being seven times thrown into captivity, compelled to flee, and stoned. After preaching both in the east and west, he gained the illustrious reputation due to his faith, having taught righteousness to the whole world, and come to the extreme limit of the west, and suffered martyrdom under the prefects. Thus was he removed from the world, and went into the holy place, having proved himself a striking example of patience.
Ignatius, writing around AD 105-115 to the Ephesians, calls Paul “the martyred.”
I know both who I am, and to whom I write. I am a condemned man, ye have been the objects of mercy; I am subject to danger, ye are established in safety. Ye are the persons through whom those pass that are cut off for the sake of God. Ye are initiated into the mysteries of the Gospel with Paul, the holy, the martyred, the deservedly most happy, at whose feet may I be found, when I shall attain to God; who in all his Epistles makes mention of you in Christ Jesus.
In his Prescription Against Heretics (circa AD 200), Tertullian seems to assert that Paul was beheaded like John the Baptist, and that it occurred at Rome.
Since, moreover, you are close upon Italy, you have Rome, from which there comes even into our own hands the very authority (of apostles themselves). How happy is its church, on which apostles poured forth all their doctrine along with their blood! where Peter endures a passion like his Lord’s! where Paul wins his crown in a death like John’s! where the Apostle John was first plunged, unhurt, into boiling oil, and thence remitted to his island-exile!
In his Church History Book II Chapter 25:5-8 (AD 320), Eusebius cites the testimony of Caius, a member of the church in Rome, and the writing of Dionysius.
Thus publicly announcing himself as the first among God’s chief enemies, he was led on to the slaughter of the apostles. It is, therefore, recorded that Paul was beheaded in Rome itself, and that Peter likewise was crucified under Nero. This account of Peter and Paul is substantiated by the fact that their names are preserved in the cemeteries of that place even to the present day.
Sometimes the historical references do not exactly agree (though that is not unusual for historical accounts). The early reference by Clement states that Paul suffered martyrdom under the prefects, while later Eusebius says that Nero had Paul beheaded in Rome. That does not mean these accounts cannot be harmonized. Perhaps the prefects were operating under the authority of Nero, and being beheaded is a form of martyrdom.
One may accept or reject the accuracy of these accounts. (I have some question about the reliability of Peter’s presence in Rome, period.) However, the accounts exhibit that there was an early tradition of Paul being a martyr (circa AD 96) and that this occurred in Rome by beheading (AD 110-200).