The battle was a decisive event for the subsequent history of the Balkans.
With the collapse of the Epirote–Latin league, Michael Palaiologos was free to pursue the reconquest of Constantinople and the revival of the Byzantine Empire: the rump Latin Empire was now cut off from any aid, and the capture of Villehardouin deprived it, in the words of Donald Nicol, "of its only capable defender".
Already in 1260, Michael Palaiologos attacked Constantinople, as one of the knights taken prisoner in Pelagonia, and whose house was in the city walls, had promised to open a gate for the emperor's troops.
He failed to do so, and Palaiologos launched an unsuccessful assault on Galata instead.
Constantinople was finally captured, almost by chance, by Alexios Strategopoulos on 25 July 1261, allowing for the re-establishment of the Byzantine Empire under the Palaiologos dynasty.

The Nicaean victory at Pelagonia also led to immediate, but short-lived, territorial expansion in Greece: John Palaiologos invaded Thessaly and the Duchy of Athens up to Thebes, while Alexios Strategopoulos and John Raoul Petraliphas were tasked with reducing Epirus proper.
Strategopoulos and Petraliphas crossed the Pindus Mountains, bypassed Ioannina, which they left under siege, and captured the Epirote capital, Arta, forcing Michael II to flee to the island of Cephalonia.
At Arta they found and released many Nicaean prisoners, including Akropolites.
In the next year, however, the Nicaean successes were largely undone: John Doukas defected back to his father, and Michael II with an Italian mercenary army landed at Arta, and the Epirote population rallied to his cause.
The Epirotes routed the Nicaeans, and Strategopoulos himself was captured and briefly held prisoner.

The battle was a particularly heavy blow to the Principality of Achaea.
It was the first heavy defeat it had ever suffered, and at a stroke lost most of its soldiers and a greater part of its nobles.
Alongside the Prince, his close relatives Anselin of Toucy and Geoffrey of Briel were also captured.
As a result, the entire Morea peninsula was also opened up to Michael Palaiologos' ambitions.
The emperor offered to set free Villehardouin and his nobles and provide for comfortable retainers for them, if they were to hand over the Principality to him; and while Villehardouin refused this offer, after the fall of Constantinople he finally agreed to hand over a number of fortresses and swear an oath of allegiance to Palaiologos in exchange for his freedom.
This was ratified by the so-called "Parliament of Ladies" (as most of the male nobles of Achaea were prisoners), and in early 1262 Villehardouin was released, and the forts of Monemvasia and Mystras, as well as the district of Mani, were handed over to the Byzantines.
From there the Byzantines would launch repeated attempts to conquer Achaea, and although these failed for the moment, they were extremely costly to the Achaeans, and the foothold gained by the Byzantines in the region would form the nucleus of the future Despotate of the Morea, where Byzantine culture enjoyed its last flowering before the Ottoman conquest.

The defeat at Pelagonia also ended the supremacy of the Principality of Achaea in the affairs of Frankish Greece, and the Nicaean/Byzantine offensive that followed further curtailed its political independence.
No longer able to confront the resurgent Byzantines, Prince William turned to the successors of Manfred of Sicily, the Angevins of Naples, for aid, as, faced with a common enemy, did the Greek rulers of Epirus and Thessaly.
The result was the Treaty of Viterbo in 1267, after which, in the words of the historian Peter Lock, "The Frankish states of the Aegean [...] became virtual marcher lordships of the Angevin kingdom of Naples and no longer lordships in their own right.
They become subsumed in the power politics of the Mediterranean as viewed from a Neapolitan perspective".
The battle was a decisive event for the subsequent history of the Balkans. With the collapse of the Epirote–Latin league, Michael Palaiologos was free to pursue the reconquest of Constantinople and the revival of the Byzantine Empire: the rump Latin Empire was now cut off from any aid, and the capture of Villehardouin deprived it, in the words of Donald Nicol, "of its only capable defender". Already in 1260, Michael Palaiologos attacked Constantinople, as one of the knights taken prisoner in Pelagonia, and whose house was in the city walls, had promised to open a gate for the emperor's troops. He failed to do so, and Palaiologos launched an unsuccessful assault on Galata instead. Constantinople was finally captured, almost by chance, by Alexios Strategopoulos on 25 July 1261, allowing for the re-establishment of the Byzantine Empire under the Palaiologos dynasty. 
The Nicaean victory at Pelagonia also led to immediate, but short-lived, territorial expansion in Greece: John Palaiologos invaded Thessaly and the Duchy of Athens up to Thebes, while Alexios Strategopoulos and John Raoul Petraliphas were tasked with reducing Epirus proper. Strategopoulos and Petraliphas crossed the Pindus Mountains, bypassed Ioannina, which they left under siege, and captured the Epirote capital, Arta, forcing Michael II to flee to the island of Cephalonia. At Arta they found and released many Nicaean prisoners, including Akropolites. In the next year, however, the Nicaean successes were largely undone: John Doukas defected back to his father, and Michael II with an Italian mercenary army landed at Arta, and the Epirote population rallied to his cause. The Epirotes routed the Nicaeans, and Strategopoulos himself was captured and briefly held prisoner.
The battle was a particularly heavy blow to the Principality of Achaea. It was the first heavy defeat it had ever suffered, and at a stroke lost most of its soldiers and a greater part of its nobles. Alongside the Prince, his close relatives Anselin of Toucy and Geoffrey of Briel were also captured. As a result, the entire Morea peninsula was also opened up to Michael Palaiologos' ambitions. The emperor offered to set free Villehardouin and his nobles and provide for comfortable retainers for them, if they were to hand over the Principality to him; and while Villehardouin refused this offer, after the fall of Constantinople he finally agreed to hand over a number of fortresses and swear an oath of allegiance to Palaiologos in exchange for his freedom. This was ratified by the so-called "Parliament of Ladies" (as most of the male nobles of Achaea were prisoners), and in early 1262 Villehardouin was released, and the forts of Monemvasia and Mystras, as well as the district of Mani, were handed over to the Byzantines. From there the Byzantines would launch repeated attempts to conquer Achaea, and although these failed for the moment, they were extremely costly to the Achaeans, and the foothold gained by the Byzantines in the region would form the nucleus of the future Despotate of the Morea, where Byzantine culture enjoyed its last flowering before the Ottoman conquest.
The defeat at Pelagonia also ended the supremacy of the Principality of Achaea in the affairs of Frankish Greece, and the Nicaean/Byzantine offensive that followed further curtailed its political independence. No longer able to confront the resurgent Byzantines, Prince William turned to the successors of Manfred of Sicily, the Angevins of Naples, for aid, as, faced with a common enemy, did the Greek rulers of Epirus and Thessaly. The result was the Treaty of Viterbo in 1267, after which, in the words of the historian Peter Lock, "The Frankish states of the Aegean [...] became virtual marcher lordships of the Angevin kingdom of Naples and no longer lordships in their own right. They become subsumed in the power politics of the Mediterranean as viewed from a Neapolitan perspective".
Battle of Pelagonia