After his victory at Tippermuir and the capture of Perth, the Marquis of Montrose received news that the Marquis of Argyll was marching from Stirling with a large Covenanter force. Anxious to keep up the momentum of his campaign, Montrose left Perth on 4 September 1644 and marched north-east along the Firth of Tay. The well-defended burgh of Dundee was summoned to surrender but refused, so Montrose continued towards Aberdeen. Most of the Highland clansmen departed with their plunder after Tippermuir, and Lord Kilpont's men disbanded after Kilpont himself was murdered by his own second-in-command, Stewart of Ardvorlich. However, Montrose was joined by two troops of horse under Nathaniel Gordon and Sir Thomas Ogilvy.
Having refused the summons, a Covenanter force under the command of Lord Balfour of Burleigh marched out and deployed along the crest of a flat-topped ridge about half-a-mile south of the burgh. The ridge topped the northern slope of the How Burn valley and overlooked a complex of buildings and ponds known as Justice Mills at its western end. Burleigh's infantry comprised around 2,000 men: two regular Covenanter regiments (his own and Lord Forbes'), the Aberdeen militia and some local levies. He also had around 300 cavalry, including three troops of regulars, which were deployed on the flanks.
Montrose drew up on the opposite side of the valley with the burn separating the two armies. MacColla and Montrose were in the centre of the Royalist line at the head of the three Irish regiments. Musketeers and two dozen horse were placed on each wing to hamper the Covenanter cavalry. Sir William Rollo commanded the Royalist right flank; Colonel Hay, a professional soldier who had served with Lord Huntly, commanded the left.
The battle opened when Colonel Hay advanced to drive a detachment of Covenanter musketeers out of Justice Mills. A counter-attack by Captain Keith's troop of horse was thrown back and a firefight developed as Covenanter musketeers moved up to contest the position. Sir William Forbes of Craigevar advanced with fifty Covenanter horse to attack Manus O'Cahan's regiment on the left of the Royalist centre. The musketeers coolly opened their ranks to let the Covenanters ride through then turned and fired a volley into their backs. Nathaniel Gordon's Royalist horse charged and routed the disordered Covenanters, capturing Craigevar and his second-in-command. On the right wing, Lords Crichton and Fraser led Covenanter cavalry attacks against Sir Thomas Ogilvy's Royalist horse and MacDonnel's Irish regiment. Although the Covenanter attacks on both wings were largely ineffective, they succeeded in keeping O'Cahan's and MacDonnel's regiments pinned down and unable to join the Royalist attack in the centre, where Montrose and MacColla led Laghtnan's regiment up the steep slope against Burleigh's main position. After a brief firefight, the Irishmen threw down their muskets and charged with swords and dirks into the Covenanter centre. The line collapsed immediately as the militiamen turned and ran back towards the town, pursued and slaughtered in the streets by the furious Irishmen.
The burgh of Aberdeen was subjected to a three-day orgy of murder, pillage and rape which Montrose made no attempt to stop. He may have wanted to make an example of Aberdeen for resisting him, but the atrocities committed there greatly damaged his cause. On hearing that the Marquis of Argyll's pursuing army was advancing from Brechin, Montrose read the King's proclamation against the Covenant and withdrew towards the Highlands.
Argyll occupied Aberdeen on 19 September with a force of 4,000 foot and 900 horse. During September and October 1644, the Covenanters pursued the Royalists across large tracts of north-eastern Scotland. Argyll sent a large detachment to secure Inverness, while Montrose's much smaller force was further weakened when Alasdair MacColla insisted upon marching away to recruit in the western Highlands, taking 500 of his men with him. Montrose tried to raise the Royalist Gordon clan around their stronghold of Strathbogie (now called Huntly). He was joined by a few hundred clansmen but his efforts were hampered by the continued absence of the clan leader the Marquis of Huntly and by the fact that Huntly's eldest son Lord Gordon had sided with the Covenanters.
On 28 October, Argyll finally caught up with Montrose at Fyvie Castle in Aberdeenshire. Skirmishing continued for several days in the vicinity of the castle but Montrose maintained a strong defensive position and Argyll was unable to bring the smaller Royalist force to battle. When Argyll withdrew to find fodder for his cavalry horses, Montrose took the opportunity to escape across the hills to Blair Atholl. As many of Montrose's followers were deserting him, Argyll marched back to Edinburgh, convinced that the Royalist uprising would fade completely with the onset of winter.