Fernando did not cherish resentment against the rebellious town. He called a Cortes here in 1178, and liberally endowed the see. In gratitude for the royal favour, Bishop Vital upheld the marriage of Alfonso IX. with his cousin, Teresa of Portugal, thereby bringing upon himself the fulminations of Pope Celestine III., and ultimately the sentence of suspension and deposition. Meanwhile the fighting spirit of the Salamancans was gratified by the establishment of the military order of Alcantara by two of the townsmen, Don Suero Fernández and his brother Gomez. The knights attached themselves to the Cistercian Order, their headquarters being the hermitage of San Julian de Pereo, on the banks of the Coa. The order was approved in 1177 by a bull of Pope Alexander III., afterwards confirmed by Lucius III.
Alfonso IX. endowed Salamanca with the university, which was destined to make its name known to the utmost confines of Christendom. This was a flourishing time in Salamanca. The Dominicans and Franciscans settled in the town; buildings, colleges, churches, and convents sprang up on all sides. The banner of Salamanca was seen in the forefront of the battle at Caceres, at Montanchez, at Merida; it fluttered over fallen Trujillo and Medellin; it waved before the walls of Ubeda in 1234, and of Granada two years later. The townsmen followed the Infante Alfonso to the sieges of Murcia and Seville (1248) and were rewarded for their valour by the privilege of holding open markets--probably heretofore the prerogative of the governor.
To these halcyon days there succeeded for Salamanca a long period of discord and warfare. Sancho el Bravo, when prince, held the town against his father; and in 1288 it was severely punished for its loyalty to the king by the rebellious Infante Don Juan, whose father-in-law, Don Lope de Haro, seized on the citadel. Under its walls halted the Portuguese army of King Diniz, marching upon Valladolid. In 1308 Salamanca made a vigorous defence, in the interests of the Queen Regent, Maria de Molina, against Nuñez de Lara.
The city is honourably distinguished by the refusal of the ecclesiastical council, held here in 1310, to condemn the doomed order of Knights Templars, who were, however, despoiled of their property here as elsewhere by decree of the Council of Vienne. A more cheerful function, the year following, was the baptism of the Infante Alfonso, born here, August 13, 1311. The lordship of his native city was afterwards given by this king to his wife, Maria of Portugal. The Salamancans fought well at the battle of the Salado (1340) under their bishop Juan Lucero. It was this prelate who in 1354 dissolved the marriage of Pedro the Cruel with Blanche of Bourbon, and celebrated the king’s amazing union with Juana de Castro, whom he repudiated on the following day. Lucero’s successor, Alfonso Barrasa, was a fervent partisan of Enrique de Trastamara. He followed him to the field with a force of five hundred archers, and held the city against his enemies. Meanwhile the Tejadas, one of the most powerful families of Salamanca, had declared for Don Pedro, and threw themselves into Zamora. The town was taken by Enrique’s partisans, while Don Alfonso Lopez de Tejada retired to the citadel, leaving his sons in the hands of the enemy. On their father’s refusal to surrender, the miserable lads were put to death. Don Alfonso escaped to Portugal, where he did not return till the reign of Juan I. He died in his native city in the year 1404. Bishop Barrasa on the triumph of Enrique II. was liberally rewarded for his devotion, and entrusted with important and honourable embassies to Flanders and Italy.