Although Josephine went on buggy rides with the president and stayed with him in the house, it was Nuttall's responsibility to dress, feed, and shave the ailing president. "I spent considerable of the day in the Presidents room fanning him and changing him," a typical diary entry reads. After passing in and out of consciousness for several months, the church president died in July 1887. He was succeeded by Wilford Woodruff, who likewise required the secretarial and nursing skills of the John Nuttall.

An interesting occurence for Nuttall was in 1889 when President Woodruff summoned him to his office to receive dictation:

After he had concluded writing, which he was doing when I arrived, he asked me to copy a Revelation which he had received. I did so . Having heard Bro J[ohn] W Youngs reasoning [that the practice of plural marriage should be discontinued], I felt very much worked up in my feelings for I did not feel that as a church we could assume the position in regard to Celestial marriage which he seemed to desire should be taken, and when Prest Woodruff commenced talking to me this evening I felt that he had become converted and [I] actually trembled, for I know such had not been Prest Woodruffs feelings before, but as I wrote at his dictation, I felt better all the time and when completed I felt as light and joyous as it is possible to feel, for I was satisfied that Prest Woodruff had received the word of the Lord. When Prest Jos. F. Smith returned and read the revelation he was moved to tears and expressed his approval and acceptance of the word of the Lord to His Servants & Saints. We all felt well and thankful to the Lord. Prest Woodruff remained with us at the Gardo House tonight.

The revelation confirmed the continuance of polygamy less than a year before the Manifesto would reverse that determination. In 1889 the issue of concern was a federal challenge to Mormon citizenship because of suspicion that Mormons swore an oath of vengeance against the United States as part of the temple ceremony. As the church presidency and Twelve discussed how to respond, one suggestion was to send one of the apostles to court to quote, for the judge's benefit, from the Book of Revelation: "How long, O Lord, holy and true, dost thou not judge and avenge our blood on them that dwell on the earth?" Ultimately the judged ruled against the church, and evidence elsewhere indicates that the wording of the so-called "oath of vengeance" was subsequently altered so no one would misconstrue it to imply an intent to commit acts of treason against the nation.

A further item of note in this remarkable diary is that Nuttall appears to have taken a third wife in 1891, either for "time" (this life) or "eternity" (the hereafter), where he writes that he "met with Sister C in the sealing room & we confirmed our covenant with each other." Throughout his diary, Nuttall cryptically refers to Catherine Ann Conover as "Sister C," "C. A. C.," and "C. A. Hunt" rather than her actual name. Conover was previously married to Joseph Hunt but had separated from him. The ceremony, whatever it was, was approved by Apostle Anthon H. Lund and performed by Daniel H. Wells, according to the diary. Shortly after Nuttall's death, the marriage was re-consecrated by proxy in the Manti Temple.