Johnson served in the Colored Regiment until the end of the Civil War, after which he moved to Ontario, Canada, and began working as a mason and stonecutter. In 1874, he married Theodocia Allen, with whom he had seven children. 

In 1884, Johnson and his family moved to Waddington, New York, where Johnson did the masonry work on Waddington's Town Hall.  That same year, Johnson led the construction of the Chamberlain Corners bridge on the Grass River. This beautiful arched stone bridge still exists today.  Johnson built two more bridges which were removed duing the Seaway construction.

In 1890, the Johnsons settled in Ogdensburg, New York.  In 1997, Johnson fell while cutting stone in Cornwall, Ontario.  Fracturing his ankle drove his decision to apply for a disability pension.  Isaac wanted to make sure his children and others were educated on the terrible experience of slavery.  In 1904, his book entitled Slavery Days of Old Kentucky was printed privately in Ogdensburg, New York. Johnson died of a heart attack there in December 1905 at the age of 61.  

In 1995, Hope Irvin Marston wrote the book entitled Isaac Johnson From Slave to Stonecutter.  In this book, she provides history of Isaac's life after the civil war.  The book is dedicated in honor of Pauline Tedford and E. Jane Layo, Waddington Historians, who were thanked for keeping the memory of Isaac Johnson alive in Waddington.