Puerto Rico was scantily provided with priests till the year 1518, when the treasurer, Haro, wrote to Cardinal Cisneros: "There are no priests in the granges as has been commanded; only one in Capárra, and one in San German. The island is badly served. Send us a goodly number of priests or permission to pay them out of the produce of the tithes."

The "goodly number of priests" was duly provided. Immediately after the transfer of the capital to its present site in 1521, the Dominicans began the construction of a convent, which was nearly completed in 1529, when there were 25 friars in it. They had acquired great influence over Bishop Manso, and obtained many privileges and immunities from him. Bishop Bastidas, Manso's successor, was less favorably disposed toward them, and demanded payment of tithes of the produce of their agricultural establishments. He reported to the king in 1548: "There is a Dominican monastery here large enough for a city of 2,000 inhabitants,[79] and there are many friars in it. They possess farms, cattle, negroes, Indians, and are building horse-power sugar-mills; meanwhile, I know that they are asking your Majesty for alms to finish their church … It were better to oblige them to sell their estates and live in poverty as prescribed by the rules of their order."

The Franciscans came to Puerto Rico in 1534, but founded no convent till 1585, when one of their order, Nicolas Ramos, was appointed to the see of San Juan. Then they established themselves in "la Aguáda," and named the settlement San Francisco de Asis. Two years later it was destroyed by the Caribs, and five of the brothers martyrized. No attempt at reconstruction of the convent was made. The order abandoned the island and did not return till 1642, when they obtained the Pope's license to establish themselves in the capital. Like the Dominicans, they soon acquired considerable wealth.

The privilege of administering parishes and collecting tithes, which was the principal source of monastic revenues, was canceled by royal schedule June 13, 1757. The monks continued in the full enjoyment of their property till 1835, when all the property of the regular clergy throughout the Peninsula and the colonies was expropriated by the Government. In this island the convents were appropriated only after long and tedious judicial proceedings, in which the Government demonstrated that the transfer was necessary for the public good. Then the convents were used—that of the Dominicans as Audiencia hall, that of the Franciscans as artillery barracks. The intendancy took charge of the administration of the estate of the two communities, the mortmain was canceled, and the transfer duly legalized. A promised indemnity to the two brotherhoods was never paid, but in 1897 a sum of 5,000 pesos annually was added to the insular budget, to be paid to the clergy as compensation for the expropriated estate of the Dominicans in San German. Succeeding political events prevented the payment of this also. The last representatives in this island of the two dispossessed orders died in San Juan about the year 1865.

Bishop Monserrate made an effort to reestablish the order of Franciscans in 1875-'76. Only three brothers came to the island and they, not liking the aspect of affairs, went to South America.

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The first head of the secular clergy in Puerto Rico was nominated in 1511. The Catholic princes besought Pope Julius II to make it a bishopric, and recommended as its first prelate Alonzo Manso, canon of Salamanca, doctor in theology, a man held in high esteem at court. His Holiness granted the request, and designated the whole of the island as the diocese, with the principal settlement in it as the see.

The subsequent conquests on the mainland kept adding vast territories to this diocese till, toward the end of the eighteenth century, it included the whole region extending from the upper Orinoco to the Amazon, and from Guiana to the plains of Bogotá. Manso's successors repeatedly represented to the king the absolute impossibility of attending to the spiritual wants of "the lambs that were continually added to the flock." They requested that the see might be transferred to the mainland or that the diocese might be divided in two or more. This was done in 1791, when the diocese of Guiana was created, and Puerto Rico with the island of Vieyques remained as the original one.

The bishop came to San Juan in 1513, and at once began to dispose all that was necessary to give splendor and good government to the first episcopal seat in America. Unfortunately, he arrived at a time when dissension, strife, and immorality were rampant; and when it became known that he was authorized to collect his tithes in specie, the opposition of the quarrelsome and insubordinate inhabitants became so violent that the prelate could not exercise his functions, and was forced to return to the Peninsula in 1515. He came back in 1519, invested with the powers of a Provincial Inquisitor, which he exercised till 1539, when he died and was buried in the cathedral, where a monument with an alabaster effigy marked his tomb till 1625, when it was destroyed by the Hollanders.

Rodrigo Bastidas, a native of Santo Domingo, was Manso's successor. He was appointed Bishop of Coro in Venezuela in 1532, but solicited and obtained the see of Puerto Rico in 1542. He was a man of great capacity, virtuous and benevolent. He advised the suppression of the Inquisition, asked the Government for facilities to educate the youth and advance the agricultural interests of his diocese, and commenced the construction of the cathedral. He died in Santo Domingo in 1561, very old and very rich.