In 1754, Waddell was sent to Virginia under the command of Colonel James Innes, who was commander-in-chief of all colonial forces then in Virginia under the authority of the governor of that state, Robert Dinwiddie. After seeing no action, but having been promoted to captain, Waddell returned to North Carolina in late 1754, where he then spent a substantial portion of the early phase of the war that would go on to define his career as a commander supervising the construction, maintenance, and staffing of Fort Dobbs, near what is now Statesville, North Carolina. In 1756, Waddell was recruited by Virginia's Lieutenant Governor Robert Dinwiddie to serve as a "Commissioner of Peace" to the Cherokee and Catawba tribes. Waddell was the sole representative of North Carolina in these negotiations, which secured the temporary cooperation of those tribes against the French and their native allies. In 1758, Waddell, then a major, was called by General John Forbes to command a force of 300 rangers in the Forbes Expedition, with the goal of capturing Fort Duquesne. Initially acting as scouts and camp guards, Waddell's rangers were among several advanced units ambushed on 14 September 1758, by a raiding party of Shawnee and Delaware warriors. Waddell's unit successfully defended itself, although other units that were attacked simultaneously broke and fled. On 12 November 1758, General Forbes ordered Colonel George Washington to command a force of Virginian and Carolinian troops to assault Fort Duquesne. Over the course of four days, Waddell and his troops fought off advanced groups of native French-allied warriors. By 24 November 1758, Waddell and his scouting force arrived to find that Fort Duquesne had been destroyed by the fleeing French soldiers, who had decided to abandon the fort in the face of the Forbes Expedition's methodical attack. After the conclusion of the Forbes Expedition, Waddell was given a Colonel's commission and, with his rangers, returned to Fort Dobbs to defend the Carolina territory against the increasingly belligerent Cherokee.
Anglo-Cherokee War
Waddell was stationed at Fort Dobbs on the night of 27 February 1760 when a force of Cherokee attacked the blockhouse. In the ensuing battle, which was the only battle that occurred at Fort Dobbs, between 10 and 12 Cherokee and two Provincial soldiers were wounded.
After the Treaty of Paris, Waddell led provincial militia in support of Governor William Tryon, and therefore against the "Regulation" movement during the War of the Regulation, although he did not take part in the Battle of Alamance due to having been encircled by Regulator militia near Salisbury, North Carolina. Governor Tryon's march westward to confront the Regulators was, in part, due to his desire to lift the siege on General Waddell.