He rejoined the Union Army, soon thereafter, when the Union called for more men. Upon raising and organizing the 7th Independent Company of the Ohio Sharpshooters, Squire was commissioned a captain in 1862. He served with the Seventh Ohio Sharpshooters until 1865. During the Civil War, Squire participated in the battles of Nashville, Chickamauga, Resaca, and Missionary Ridge. During the latter campaign, "Squire served as judge advocate of the general courts martial. Later Squire was made judge advocate of the district of Tennessee," with headquarters in Nashville. "He served on the staff of Major General Rousseau as judge advocate and also under Major General Thomas during the siege and battle of Nashville." In 1865, he was discharged with the rank of captain and was subsequently Brevetted major, lieutenant colonel, and colonel.