Colors of Chaos (1998) by L.E. Modesitt Jr....?
It's the ninth book in the Saga of Recluce series.
Ceryl, now a full mage in The White Order, must prove himself indispensible to Jeslek, the High Wizard. Whether through assassination, effective gorvernance of occupied territory or the fearless and clever direction of troops in battle, Ceryl faces many harrowing obstacles, not the least of which is Anya, the plotting seductress who's the real power behind the scenes of the white wizards. With his wits, his integrity, and the support of his love, the Black healer Leyladin, he must survive long enough to claim his rightful spot within the ruling heirarchy of the White Order.
This excerpt from a review notes that the plot involves mages, armies, and conflict between various cities.
As Colors of Chaos opens, Cerryl is a full mage, but low in the guild's pyramid of power. As a gate mage, he's charged with inspecting wagons as they enter the city.
Traditionally, the enemies of the White Mages have been the "Blacks," the practitioners of magic based on order. But as Cerryl spends day after day on guard duty, he begins to realize that the guild faces a far more dangerous enemy: economics. Revenues on the roads maintained by the guild are falling as other cities use the highways but refuse to pay their fair share to maintain them. The guild's leadership tries to bully the other cities, raising armies and mountains in an attempt force them into line.
Searching through the Google Books preview, I've also found passages indicating that specific colours are associated with specific cities, such as "the White City of Fairhaven", "the green of Certis" and "the cyan of Lydiar."
There's also a large-scale battle toward the end of the book, with fire magic being directed at enemy troops clad in blue.
"Chaos fire—on the right!"
Cerryl obliged, trying to ignore the growing headache, the knives that cut through his skull with each new attempt at flinging chaos fire.
The White horse, now a mixture of forces from Certis, Gallos, and Hydlen, charged up the left side of the hill toward the crest. A few scattered arrows flew toward the lancers, but only a handful of riders fell.
Jeslek summoned another firecloud, searing the area of the earthworks to the northeast from where some of the remaining blue archers had loosed shafts. No more arrows rose from the blue bows.