The Early Modern Age was marked by increasing tension between the power of the Spanish Monarchy and those of the regions. The appointment of a Castilian as Viceroy in 1590, contrary to the agreement all Royal officials be Aragonese caused widespread unrest; when the Madrid authorities attempted to arrest the Aragonese writer and politician Antonio Perez in May 1591, it caused street violence in Zaragossa and a revolt known as the Alterations of Aragon. The unrest was largely confined to Zaragossa and quickly suppressed, with Perez going into exile. Philip then ordered a reduction in the proportion of taxes retained by the Generality of Aragon to lessen their capacity to raise an army against him.

The decay of independent institutions meant political activity focused instead on the preservation of Aragonese history, culture and art. The Archive of the Kingdom of Aragon preserved legal documents and records from the Justiciar and the Palace of Deputation or Parliament, unfortunately largely destroyed by the French in the battles of 1809. Debates on the causes of the 1590/91 revolt became a contest between opposing views of history that arguably persist in modern Spain.

The new emphasis on Aragonese history led to the creation of the position of Chronicler or Historian of Aragon; its holders included Jerónimo Zurita y Castro, the De Argensola brothers, Bartolomé and Lupercio, Juan Costa and Jerónimo Martel. Much of the work produced by Aragonese writers challenged Philip II’s version of events and were censored by the central government. In retaliation, the Generality of Aragon ordered the work of Castilian historian Antonio de Herrera y Tordesillas to be burned and commissioned Vicencio Blasco de Lanuza to write an alternative. His ‘History of Aragon’ was published in two volumes, 1616 and 1619 respectively; the urgency shows the importance placed on responding to Herrera. Other works commissioned at this time for the same purpose include a History of the Aragonese Deputation by Lorenzo Ibáñez de Aoiz and a detailed cartography of the Kingdom of Aragon by João Baptista Lavanha.

In 1590/91, the Spanish monarchy was at the height of its strength but during the 17th century Spanish power declined for a number of reasons. Famine, disease and almost continuous warfare, largely in the Spanish Netherlands drained money, energy and men and weakened the economy; it is estimated the population of Spain fell nearly 25% between 1600 and 1700.

War and economic decline inevitably led to increases in taxes, with predictable results; the refusal of the Catalan Cortes to contribute their share of the 1626 Union of Arms eventually led to a full-scale revolt in 1640. While Aragon itself remained relatively peaceful, it had to be treated with care by the Madrid government; during the reign of Charles II from 1665 to 1700, it provided his half-brother John of Austria with a power base in his battle for control of government with the Queen Regent Mariana of Austria.

During the 1701–1714 War of the Spanish Succession, Aragon, Catalonia, Valencia and Majorca supported the Austrian claimant Charles. The victory of Philip V accelerated the trend towards greater centralisation; the Nueva Planta decrees of 1707 abolished the fueros and Aragonese political structures with their powers transferred to the Deputation of the Kingdom in Madrid; Aragon and Valencia were brought into the system in 1712, Catalonia and Majorca following in 1767.