The end of the book of Acts leaves us in suspense about what happens to Paul. Scholarship is divided, as usual, about Paul’s subsequent years, but here are some ideas.
Clinton Arnold, in John, Acts: Volume Two (Zondervan Illustrated Bible Backgrounds Commentary), offers the following:
At the conclusion of his writing, Paul still has not faced his trial. Had Paul already been released, it is difficult to explain why Luke would not have recorded the outcome of the trial (unless he was planning to do so in a third volume—a work never completed). Paul has been in custody four years, and his readers await the anticipated acquittal by the emperor. It would have made a better ending to the Gospel and Acts to portray Paul as free from chains and proclaiming the gospel to Gentiles in regions beyond Rome.
One of the activities Paul engages in during this time is letter writing. From his Roman apartment chained to a soldier, he writes Philippians (if it was not written while he was in prison in Caesarea, or even earlier during his Ephesian ministry), Colossians, Philemon, and Ephesians. Philippians may plausibly be explained as having been written just before Paul’s trial at the end of the two years since it reflects an approaching crisis that could end in life or death for the apostle (Phil. 1:19-26).
Stanley Toussaint, in The Bible Knowledge Commentary, writes,
Perhaps no charges were filed in Rome and Paul was released. The Jews would know they had no case against Paul outside of Judea and so would be reluctant to argue their cause in Rome.
Probably Paul returned to the provinces of Macedonia, Achaia, and Asia and then turned west to Spain according to his original plans (Rom. 15:22–28). Then he ministered once more in the Aegean area where he was taken prisoner, removed to Rome, and executed.
An article on gotquestions.org called “How did the apostle Paul die?” answers this way:
The Bible does not say how the apostle Paul died. Writing in 2 Timothy 4:6–8, Paul seems to be anticipating his soon demise: ‘For I am already being poured out as a drink offering, and the time of my departure has come. I have fought the good fight, I have finished the race, I have kept the faith. Henceforth there is laid up for me the crown of righteousness, which the Lord, the righteous judge, will award to me on that Day, and not only to me but also to all who have loved his appearing.’
Second Timothy was written during Paul’s second Roman imprisonment in AD 64—67. There are a few different Christian traditions in regards to how Paul died, but the most commonly accepted one comes from the writings of Eusebius, an early church historian. Eusebius claimed that Paul was beheaded at the order of the Roman emperor Nero or one of his subordinates. Paul’s martyrdom occurred shortly after much of Rome burned in a fire—an event that Nero blamed on the Christians.
Adding more details is a 2009 article titled “New Discoveries Relating to the Apostle Paul” at biblearchaeology.org. Speaking of Christian monuments in Rome, Brian Janeway writes:
But lesser known are those relating to the Apostle Paul, who was martyred in Rome at the conclusion of what most believe was a second imprisonment postdating the book of Acts, between which he traveled to Spain and Crete (Titus 1:5). Of this period, the 3rd century church historian Eusebius wrote:
‘After defending himself the Apostle was again set on the ministry of preaching…coming a second time to the same city [Paul] suffered martyrdom under Nero. During this imprisonment he wrote the second Epistle to Timothy’ (Eccl Hist. 2.22.2).
Paul’s poignant and triumphant words are preserved in chapter 4: ‘For I am already being poured out as a drink offering, and the time for my departure has come. I have fought the good fight, I have finished the course, I have kept the faith’ (2 Tim. 4: 6-7).
Eusebius goes on to report ‘that in his [Nero’s] time Paul was beheaded in Rome itself and that Peter was likewise crucified. (Eccl Hist. 2.25.5) Paul’s execution took place at the end of Nero’s reign, c. A.D. 65-68. His legal status as a Roman citizen protected him from the ignominious sentence of crucifixion suffered by Peter.
The traditional spot for the beheading is known as the Abbey of the Three Fountains (the head reputedly bounced three times before coming to rest), which is south of the modern center of Rome. Early reports stated he was laid in the family tomb of a devout Roman noblewoman named Matrona Lucilla. His remains may have subsequently been hidden in catacombs for safekeeping during Vespasian’s reign (see below). Nearby the abbey is the monumental Church of San Paolo Fuori Le Mura (St. Paul Outside the Walls) where the remains of Paul are entombed.