He was tasked with prosecuting the Bald Hills War against the Indians in the counties of northwestern California.

Colonel Lippitt and his regimental headquarters was transferred to Benicia Barracks, July 20, 1863, and from there to Fort Miller, Fresno County, California, August 11, 1863, where they were stationed until October 1, 1864.

There during the month of October 1864, Colonel Lippitt was mustered out with men of his regiment who had completed their terms of enlistment.

Following the civil War, General Lippitt wrote four military books, A Treatise on the Tactical Use of The Three Arms, Infantry, Artillery, and Cavalry in 1865, A treatise on intrenchments in 1866, The Special Operations of War: comprising the forcing and defence of defiles; the forcing and defence of rivers in retreat; the attack and defence of open towns and villages; the conduct of detachments for special purposes; and notes on tactical operations in sieges in 1868, and Field service in war: Comprising marches, camps and cantonments, outposts, convoys, reconnaissances, foraging, and notes on logistics in 1869.

In 1902 he published his autobiography, Reminiscences of Francis J. Lippitt, written for his family, his near relatives and intimate friends.