In 1856, he became assistant principal at the West Newton English and Classical School in Massachusetts, headed by his cousin Nathaniel Topliff Allen.

In 1863–4, during the Civil War, William and his wife Mary ran a school for newly emancipated slaves on the Sea Islands of South Carolina.

He returned to the Lambert family home in West Newton, MA in 1865 in time for the birth of their daughter Katherine, followed by the death of his wife Mary one month later.

[2] His daughter Katherine Lambert Allen joined him and his new family in Wisconsin: she later earned a bachelor's degree (1887) and PhD (1898) and became an instructor at the university.

The Slave Songs of the United States (1867), of which he was joint-editor with Charles Pickard Ware and Lucy McKim Garrison, was inspired by his work among the freedmen and the first book of its kind ever published.