In 1564 the president arrived in state with all the trappings appropriate to his high rank. His powers were most ample; he was practically vicegerent of the Castilian king; his jurisdiction extended not only over the BogotÁ-Pamplona plateaux and Tolima on the upper Magdalena, but also over Santa Marta, Cartagena, Antioquia, and even to Panama and the Mosquito coast. The name of New Granada, which Quesada had given to his conquests in honor of his native province in Spain, was extended to the whole presidency. To it were also attached, though loosely, the provinces that now make up the republic of Venezuela. But access to the Venezuelan coast from BogotÁ was so difficult as to prevent that region from ever being really a part of the New Granada presidency, and it became an independent captaincy-general in 1731. The eastern boundary of the president's immediate jurisdiction included the provinces which naturally communicated with the Colombian plateaux, but the extension of the Andes north-east from Pamplona along the Venezuelan coast was left to be settled from Coro. For similar reasons the valley of the upper Cauca—Cali and Popayan, as well as Pasto—was attached to the presidency of Quito, and the subordination of its governor to BogotÁ was only incidental and gave rise to many disputes and conflicts. The administrative entity of New Granada may be said to have included the territory which the Spaniards had reached by the line of the Magdalena, and in addition the Cartagena region and the Isthmus. The last named province was a source of constant trouble, because the difficulties of communication and the diversities of interests really made it separate from the rest of New Granada. Panama's governor and independent audiencia frequently defied the commands received from BogotÁ.

The disorders near BogotÁ ceased after the arrival of the first president, Neiva. He actively engaged in promoting new colonisation, founding the city of Ocana in the Maracaibo watershed north-west of Pamplona, as well as Leiva and several other towns. He opened a road down from BogotÁ to Honda at the head of navigation on the Magdalena, and in his time great flatboats were introduced. These were poled against the river's rapid current, and they continued the sole means of river freight transportation for nearly three centuries. The cornerstone of the BogotÁ cathedral was laid, and schools established which soon counted among the most successful and famous in Spanish America. The country prospered after a fashion. The fertile plateaux from BogotÁ to the north were admirably adapted to the residence of Europeans, and the rich soil soon produced large crops of wheat and fed great herds of cattle. This region was so attractive that the Spaniards became attached to the country and contentedly established themselves as semi-feudal proprietors of estates cultivated by the docile and industrious Indians. A considerable proportion of the successive generations of office-holders sent out from Spain, applied for land-grants and remained in the country, founding new Creole families. Mixture with the aborigines occurred on a large scale and the process of Caucasianising the population made greater progress than in many other parts of Spanish America. The region was too far from the sea-coast to attract haphazard adventurers or to serve as a Botany Bay for convicts; the Spanish settlers belonged as a rule to good families; and the standard of living, education, and manners was exceptionally high. BogotÁ became one of the principal centres of Spanish American culture, and Colombian authors are celebrated for their excellence throughout the Spanish-speaking world. In the invigorating climate the Creoles retained their physical vigour and the concentration of population on these densely inhabited plateaux increased their mental alertness. Living, however, as a superior class in the midst of a subject population, they acquired no taste or capacity for commerce or industry. A Creole was by birth a gentleman and exempt from manual labour. The Colombian plateaux made little material progress, and settled down into an eventless, patriarchal existence.

Conditions were entirely different in the deep, hot valleys of the Magdalena and Cauca and on the sweltering sea-coast plain. The semi-savage Indians did not make good labourers, and were massacred or driven into the fastnesses on the mountain sides, while their places were taken by negro slaves. The white population fell into much the same position as it occupies in the West Indian Islands. In the mining regions the Indians were pretty nearly exterminated. Antioquia, the great mineral province, has always contained a larger proportion of white blood than any other part of Colombia, and with the decline of its mines it became a centre whence white emigration poured into the other departments. Still different conditions prevailed in the extreme south, where the highlands of Popayan and the dry, cold tablelands of Pasto offered the same aspect as adjoining Ecuador. In those utterly isolated and comparatively unattractive regions the Indian population remained predominant.

In Colombia, as in all the other Andean countries, the impulse toward conquest, expansion, and colonisation seems to have died out completely with the disappearance of the first generation of conquistadores. We read of the foundation of new cities from time to time, but it usually means that previously existing villages were given municipal charters. After one brief spurt the Spaniards settled down to enjoy the fruits of their ancestors' heroic marches and battles. Except near Panama the rainy Pacific coast was left untouched, and the forests of the Amazon in the south-east could not be penetrated. The open prairies of the Orinoco north-east of BogotÁ could be occupied and the province of Casanare at the foot of the eastern Andean range became a stock region, inhabited by the same hard-riding, semi-civilised llaneros as the adjoining Venezuelan plains.

The Spanish government applied its restrictive colonial system with the utmost rigour. The obnoxious market tax was imposed as early as 1690; tobacco and salt were made monopolies; the exportation of agricultural products was discouraged; and the production of gold, emeralds, platinum, and silver, was jealously watched and heavily taxed. In the early history of the colony the profits of mining were prodigious, but during the seventeenth century, after the cream of the surface placers had been skimmed, progress was slow. The unhealthful climate of the mining regions almost exterminated the settlers; the native population diminished so rapidly that soon the mines were short-handed; and the importation of negro slaves was so costly that the smaller proprietors could not operate on their own account, and even the great mine owners had to be content with moderate profits. One-fifth of the gross product was required to be paid to the government, and there were other fiscal exactions. The efforts of the authorities to prevent the smuggling of gold introduced a swarm of soldiers, collectors, and guards with whom the miners were in a constant turmoil.

The influence of the Church was very powerful, and the population became devotedly Catholic. Great tracts of the best lands were given to the bishoprics and the religious orders. Piously disposed persons left property in trust charged with the payment of so many dollars a year for the saying of so many masses, and the stewardships, or rights to administer these estates, were the subject of sale or descended from father to son. In 1630, a daring president, Jiron, presumed to arrest and banish the archbishop of BogotÁ, but fifty years later one of his successors wrote back to Spain that "in New Granada there is much Church and little king." The poor Indians were decimated not only by war, massacre, and forced labour in the mines, but the white man's diseases played havoc with them. The small-pox was introduced on the plateaux within a few years after the conquest, and continued to ravage the country throughout the early part of the seventeenth century. The third president died of the leprosy within a few months after his arrival in 1579, and the first case of elephantiasis, which has proved a curse to Colombia, occurred in 1646.

The quarrels and disagreements between the president and the governors and audiencias of the associated provinces, especially Panama, to say nothing of the disputes with the president of Quito and the governor of Venezuela on account of conflicting jurisdiction, became so acute early in the seventeenth century that the Spanish government determined to erect New Granada into a viceroyalty, extending the power of the BogotÁ central authorities over Ecuador and Venezuela. The first viceroy was inaugurated in 1719, but he recommended a return to the old system. In the year 1740 the viceroyalty was re-established and all connection with Peru ceased. Although in the meantime Caracas had been made a captaincy-general, it was placed nominally under the viceroy's jurisdiction, and Ecuador was again detached from Lima. Within a few years the attempt to govern Maracaibo, CumanÁ, Margarita Island, and Guiana from BogotÁ was abandoned, and these provinces transferred to the Venezuelan captaincy-general. But the high rank and royal powers of the viceroys did not save them from troubles. They were engaged in an almost continual struggle against the encroachments of the clergy, while the laity protested vigorously at the constantly increasing taxation. A special royal commissioner came out in 1774 to perfect the tobacco monopoly, and five years later another agent arrived with instructions still more irritating. The Creoles of Santander arose in the "Rebellion of the Communes" and so formidable was the insurrection that the authorities were compelled to make a feint of yielding to the people's demands. They promised to expel the obnoxious commissioner; to abolish not only the tobacco monopoly, but the market-tax on the sale of domestic products, the requirement that every shipment be accompanied by a high-priced official invoice, and the poll-tax; to lower the stamp duties, the curates' tithes, and the Indian tribute; to cease burdening commerce with unreasonable highway, bridge, and ferry dues; and to require the priests to give up the practice of forcing the Indians to pay for masses. The viceroy also promised to open public employments to Creoles, to permit the establishment of a militia, and to concede to the people the right to confirm the governors nominated by the Crown or viceroy. But no sooner had the insurgents dispersed, than the government repudiated all these pledges and dragged the popular leaders to the scaffold.

The foreign commerce of the viceroyalty had diminished until only one small fleet came each year to Cartagena and Porto Bello, and though, during the latter part of the colonial period, certain viceroys did something to open up roads by which wheat, sugar, cacao, and hides could be exported at a profit, no measures could prove effective while the enormous fiscal exactions of the Spanish government continued. During the last few years of the eighteenth century, commerce was made nominally free, but this meant simply that the old prohibitions on private shipments by sea were abolished, and the ports opened for trade with Spain and the other colonies. These wise measures were, however, accompanied by such an increase in taxes that their effect was nugatory.

Meanwhile New Granada had also had her external troubles. In 1586 Sir Francis Drake reached Cartagena and forty years after the Spanish government fortified the place at great expense. Nevertheless Ducasse took it in 1695 though Admiral Vernon, with a great fleet and army, unsuccessfully besieged the place in 1741, after having captured Porto Bello. The unsettled Central American coast north from the Isthmus was nominally a part of the vice-royalty, but had been completely neglected by the BogotÁ authorities, and in 1698 a colony of twelve thousand Scotchmen, with authority from Parliament and backed by a vast popular subscription, landed on the north shore of the Isthmus. They purposed the establishment of a general emporium for all nations on the spot which the great financier, William Paterson, who originated the scheme, regarded as "the key of the commerce of the world." There was to be free-trade; the Indians were to be protected; religious liberty was to be established; and the Spanish monopoly of South and Central America destroyed. The far-sighted Paterson hoped to found a colonial empire and to enrich his own country by the resulting trade. But the enterprise was wrecked by the fatal climate and the supineness of the British Government. Provisions fell short, and within a year the survivors re-embarked in a miserable plight. Two small supplementary expeditions arrived in 1699 to find assembled a Spanish fleet and army against which no serious resistance could be made. After a little half-hearted fighting the Scotchmen capitulated and the colony was definitely abandoned. The BogotÁ government continued to neglect that coast. It was placed under the jurisdiction of the captain-general of Cuba, and the claim that Colombia set up after she became an independent nation has never held good against the Central American republics.