He first heard of The Book of Mormon and the Church of Jesus Christ of Latter Day Saints from his cousin LDS Apostle Parley P. Pratt who was seven years his senior.

According to historical records, he was chosen to be a bishop at this time to watch after the families of men who had joined the Mormon Battalion.

After arriving in the valley, at the behest of Young, Van Cott went back out on the trail to assist other companies who were having difficulties.

In 1852 Van Cott began a four-year assignment as the president of the Scandinavia Mission, headquartered in Denmark.

He is listed as being the President of the Madsen and Liljenquist companies, leading a group of Scandinavian Saints to Salt Lake in July–Sept 1862.

He died at his home a short distance south of Salt Lake City, February 18, 1883, after a lingering illness of several months.

Like several church leaders of his time, John Van Cott was instructed to practice plural marriage.