After the return of the marquis into the plain, various consultations were held as to the best plan of procedure, and it was at last determined that Ferdinand Pizarro, now lieutenant-general under the marquis, with his brother Gonzalo Pizarro as major-general, should march with the army against Cuzco196. On this occasion, a manifesto was circulated as the reason of this measure, that several of the inhabitants of Cuzco had made complaints to the marquis against the tyranny of Almagro, who had violently seized their goods and houses, and dispossessed them of their Indians and every thing that belonged to them. The marquis returned to Lima, and his brother Ferdinand marched at the head of the army towards Cuzco. Having arrived on the mountainous ridge near Cuzco in the evening, all his officers urged Ferdinand Pizarro to descend immediately into the plain that the army might encamp there for the night; but Ferdinand positively rejected this advice, and ordered the army to encamp on the mountain. Early next morning, the whole army of Almagro was seen drawn up in order of battle on the plain, under the supreme command of Orgognez; Francisco de Chaves, Juan Tello, and Vasco de Guevara, having the command of the cavalry under his orders. On the side of the mountain there was a great body of Indians in charge of a small number of Spaniards, intended to be employed as circumstances might admit in the expected battle. In the meantime, all the friends and partizans of the marquis who were in Cuzco were committed prisoners to the citadel, which was so extremely crowded on this occasion, and the places appropriated for their confinement so small, that several of them were stifled.

On the following day, after the solemnization of the mass, Ferdinand Pizarro marched his army into the plain of Cuzco in order of battle, and advanced towards the city, intending to gain possession of some high ground which overlooked the citadel. Ferdinand and his troops flattered themselves, from their great superiority in numbers, that Almagro would not risk a battle, and were even anxious to spare the effusion of Christian blood on the present occasion, in which the natives of the same country and subjects of the same sovereign were preparing to destroy each other, instead of uniting in a common cause for the general good of all. Orgognez was actuated by a different principle, and had occupied the only passage by which the troops of Pizarro could approach towards Cuzco, in which he had drawn up his troops and artillery with much judgment, under cover of a marsh, across which it was necessary for the troops of Pizarro to pass before they could attack his position. Immediately on reconnoitring the order of the enemy, Ferdinand Pizarro ordered captain Mercadillo to advance with his cavalry to a proper place for keeping the Indians in check in case they should attempt to attack his army while engaged in battle with Orgognez, and whence likewise he might be able to give succour where necessary during the approaching engagement. Before the Spaniards began to engage, the Indians on both sides skirmished with each other. The cavalry of Pizarro endeavoured to pass the morass, and being opposed by a squadron of Almagro's horse, the musketeers belonging to Pizarro advanced in front of their own horse and soon compelled the adverse cavalry to give ground. On seeing this successful commencement of the battle, Pedro de Valdivia, a maestre de campo of the marquis, assured his friends that the victory was their own. While the troops of Pizarro were passing the marsh, the Almagrians plied their artillery, and by one discharge five men belonging to Pizarro were brought down. But Pizarro pressed on under cover of a close fire from his musketeers, and passed both the marsh and a rivulet beyond, and drew up in good order on the firm ground, every one of the captains having been previously instructed how to proceed with their divisions before the engagement commenced. As Pizarro noticed that the pikemen in the army of Orgognez carried their pikes high, he gave orders to his musketeers to fire a little high, by which means in two vollies they broke above fifty of the enemies pikes197. At this time Orgognez ordered his army to advance to the charge, and observing that several of his divisions hesitated, being held in check by the fire of the musqueteers, he moved on himself at the head of his main body, directing his attack to that part of the enemy where Ferdinand Pizarro was seen at the head of his squadrons. Orgognez apparently despairing of the battle, called out while advancing, "Follow me who will! I go in the name of God to do my duty, and to seek an honourable death!" While Orgognez was advancing, Gonzalo Pizarro and Alonso Alvarado observed that his flank was uncovered, and accordingly made an immediate charge, by which above fifty of the Almagrians were overthrown. Orgognez was wounded by a musket-ball in the head, which broke through his beaver; notwithstanding which he killed two men with his lance, and wounded one of Pizarros servants in the mouth whom he mistook for the general, as he was finely dressed. For some time the engagement was extremely severe and the combatants were mingled together; but at length the troops of Pizarro forced the Almagrians to take to flight after they had a considerable number killed and wounded.

Almagro being sick, took no part in the battle, which he observed from a height at some distance, and on seeing his troops take to flight, exclaimed, "I thought we had come out to fight like valiant soldiers, not to run away like cowards." He immediately withdrew to the citadel of Cuzco, to which place he was pursued by Gonzalo Pizarro and Alonso Alvarado, and made prisoner. Orgognez was taken prisoner by two of Pizarros horsemen, who were leading him away when a third came up who bore him a grudge for some injurious treatment, and cut off his head. Several others who had surrendered were slain in this manner by personal enemies, in spite of every endeavour by Ferdinand Pizarro and his officers to protect them. The soldiers of Alvarado especially, ashamed and irritated by the defeat they had formerly sustained at the bridge of Abancay, were eager for revenge, and put many of the Almagrians to death in cold blood. Captain Ruy Dias had taken up a prisoner behind him on horseback, on purpose to protect him, when one of his own troopers run him through with his lance.

When the Indian servants of the two armies saw that the battle among the Christians was ended, they too gave over fighting, and fell to plundering the dead, whom they stripped of their clothes and valuables, even pillaging several who were yet alive, but unable to defend themselves because of their wounds; and as the conquerors were entirely taken up in pursuing their victory, the Indians had it in their power to do as they pleased, so that they entirely stripped everyone whom they found on the field of battle. The Spaniards, both victors and vanquished, were so worn out and fatigued by their exertions in this battle, that they might have been easily destroyed by the Indians who were present, if they had dared to attack them according to their original intention; but they were so busied in plundering the killed and wounded, that they neglected the opportunity of avenging themselves on their oppressors. This decisive battle was fought on the 6th of April 1538, in a plain called Cachipampa or the field of salt by the Indians, about a league to the south of the citadel of Cuzco, near a salt spring from which the inhabitants make great quantities of salt; and as these salt works are in the neighbourhood of the field, this engagement has been always known by the name of the battle of Salinas, or of the salt works198.