The Popes' power began to wane. The Fourth Crusade in 1202-1204 (https://en.wikipedia.org/wiki/Fourth_Crusade), for instance, quickly fell away from any papal control and would go on to attack Constantinople, a fellow Christian power, which earned its leaders (eventually limited to just the Venetian ones) excommunication. The Sixth Crusade in 1228–1229 was launched without (though it was organised with) papal approval, and the leader of it (Frederick II: https://en.wikipedia.org/wiki/Frederick_II,_Holy_Roman_Emperor) was in a state of conflict (including excommunication) with the pope.

The Avignon Papacy (1309-1377), when the Pope reigned from France and became increasingly under the French kings' control, and the Western Schism (1378-1418), when two rival Popes reigned simultaneously, further damaged papal authority along with other various elements of papal corruption.

Protestantism (~1517 onward) took much of Christendom out of the control of the popes, and so the Crusades were recast in terms negative to the Catholic Church (at least among the Protestants). Martin Luther wrote, "How shamefully the pope has this long time baited us with the war against the Turks, gotten our money, and destroyed so many Christians and made so much mischief! When will we learn that the pope is the devil's most dangerous cat's paw?" (The Concise History of the Crusades by Thomas F. Madden, page 192-193). Martin Luther would change his mind about the Turks when they threatened central Europe (though he was still opposed to a holy war: "If in my turn I were a soldier and saw in the battlefield a priest's banner or cross, even if it were the very crucifix, I should want to run away as though the devil were chasing me!"), but it's telling to see how far papal enmity got and the changing views on holy war.

European kings turned on each other and had other problems to deal with, and these conflicts became more important than the distant East. The Seventh Crusade (1248 to 1254) is exemplary in that, out of all the Christian states, only France at that moment was not dealing with civil war, Mongol invasions, conflict with the pope, or simply had a will to go on crusade (https://en.wikipedia.org/wiki/Seventh_Crusade).

The War of the Sicilian Vespers (1282–1302) made a concentrated counterattack against the Mamelukes at a critical moment impossible, and it lead to an inter-Christian crusade in itself (Franks and Saracens: Reality and Fantasy in the Crusades by Avner Falk, page 196). The Hundred Years War (1337-1453) between England and France monopolised much of their time and resources. France would ally itself to the Muslim Turks to fight the Christian Habsburgs beginning in 1536 (https://en.wikipedia.org/wiki/Franco-Ottoman_alliance). The aforementioned Protestant Reformation had a hand in the inter-Christian warfare as well.

European kings also became more powerful, leading to a weakening of papal authority. Sixtus V (1585-1590) wrote, "The king of Spain, as a temporal sovereign, is anxious above all to safeguard and increase his dominions ... the preservation of the Catholic religion which is the principal aim of the Pope is only a pretext for His Majesty." (The Concise History of the Crusades by Thomas F. Madden, page 324). In addition to this, the later (offensive) Crusades were mostly failures and did not profit those who participated in them.

The Black Death in 1346–53 (https://en.wikipedia.org/wiki/Black_Death) may have had a hand in it, in reducing the population of Europe there were fewer people and lesser will to go off on offensive Crusades. At least the armies were much smaller for warfare (The Concise History of the Crusades by Thomas F. Madden, page 251).

In a sense, the Crusades were simply renamed "Holy Leagues" and became defensive in nature. The last crusade to be numbered was the Ninth in 1271–1272 (https://en.wikipedia.org/wiki/Ninth_Crusade). The last pieces of the Holy Land to fall were Acre in 1291 (https://en.wikipedia.org/wiki/Siege_of_Acre_%281291%29) and Ruad in 1303 (https://en.wikipedia.org/wiki/Fall_of_Ruad).

After that, "crusades" became either minor raids (https://en.wikipedia.org/wiki/Alexandrian_Crusade), or large-scale defensive wars aimed at containing the Ottomans (https://en.wikipedia.org/wiki/Crusade_of_Varna). Eventually, these defensive crusades came to be called "holy leagues," and would go on until the threat of the Ottomans passed in about the late 1600s (The Concise History of the Crusades by Thomas F. Madden, page 193-194). Various sources actually call The Great Turkish War in 1683-1699 a "crusade," though I'm not sure if any of the participants did.

https://en.wikipedia.org/wiki/Battle_of_Lepanto

https://en.wikipedia.org/wiki/Great_Turkish_War

tl;dr: Increasingly independent kings stopped listening to the pope about going on offensive crusades, in part because it eventually stopped profiting the kings themselves, in part because they didn't respect papal authority, in part because they had to deal with more pressing matters closer to home. So the pope stopped calling for them and, with the rise of the Ottoman Empire, shifted all energies towards defense against them. These defensive wars started as crusades but eventually evolved into holy leagues. After the Ottoman threat passed in the late 1600s, they lost their reason for being and so ended.