From the final conquest in the Second Messenian War to the founding of the city of Messene after the battle of Leuktra, Messenian history is largely quiet. We know something of how the Spartans treated the Messenian helots, purging the most forward and so on, but the Messenians themselves had little impact.

There was another helot rebellion in 464 BC (the first historically firm date we have; the dates of the wars are probably late traditions and could be off by as much as a century), which is mentioned by both Pausanias and Thucydides. After a major earthquake devestated Sparta, the Messenian helots rose in rebellion and dug in on Mt. Ithome; Thucydides (1, 101-3) says that some of the perioikoi also rebelled. The Lakonians called in a number of allies, including an Athenian force under Kimon. The Athenians were called in specifically for their skill at dealing with sieges, but the Spartans grew worried that they would be a revolutionary influence and might suddenly side with the Messenians, so they sent them home again with thanks. The Athenians were offended by this and promptly formed an alliance with Argos. Thucydides says the revolt lasted ten years, but this is probably a corruption of the text. The best probable correction would be four years. In any case, once the rebellion was put down the rebels were allowed to leave the Peloponnese under truce, partly because of the difficulty of the terrain on Mt. Ithome and partly because of an oracle from Delphi warning them not to harm the supplicants of Ithomaian Zeus.

The Athenians gave the rebels the city of Naupaktos in Lokria, just across the Gulf of Corinth from the Peloponnese. Hoping to gain some territory on their own and do their new friends the Athenians a favor, the new Naupaktians attacked Oiniadai in Akarnania. They took the town and held it for a year, but were finally driven out by the Akarnanians. Naupaktos was a major Athenian ally during the Peloponnesian Wars. It was a key base for the Athenian fleet on the west side of the peninsula. Messenian slingers played a key role in the defeat and capture of the Spartans at Sphakteria in 425 BC. After that battle the Athenians settled a large Messenian force at Pylos and they staged numerous guerrilla raids into Messenia and Lakonia for several years. During the peace negotiations of 421 BC, the Spartans convinced the Athenians to withdraw the Messenian troops from Pylos and garrison it themselves.

After the war the Spartan fleet expelled the Messenians from Naupaktos. Some went to Rhegion and Sicily, where earlier Messenian refugees had gone, but most answered a call for any Greek to come join the settlement of Euhesperides in Libya.

After the Spartan power was broken at Leuktra, the Thebans invited all Messenians to return. Most did, but they refused to resettle either Andania or Oikhalia. After much consideration of the problem, Epaminondas built the city of Messene on the slopes of Mt. Ithome in 370 BC. Also at this time Epiteles the Argive is supposed to have found the rituals of the mysteries inscribed on sheets of tin where Aristomenes had buried them centuries earlier. The Messenians also decided not to expel the Nauplians from Mothone or the Asinians from the coastal regions.

The Lakonians left Messenia alone until the Phokian or Sacred War drew the Thebans away. Once the Thebans were busy elsewhere they started trying to retake the territory they had previously held. The Messenians resisted and sought allies. Eventually they allied themselves with Philip of Macedon and, as a result, stayed out of the battle of Khaironeia, not wanting to oppose the rest of Greece nor to fight against an ally.

During the Hellenistic Era, they joined in the Second Macedonian War. They did not take part in the war against the Gauls because the Lakonians refused to offer a truce for the duration. At some point they occupied Elis and put an anti-Lakonian party in power. When Demetrios, the son of Philip, attacked the Peloponnese he tried to take Messene as an easy target, but was driven out. Later, when Pyrrhos, the son of Aiakedes, attacked Lakonia the Messenians came to their aid unasked. Thereafter, relations between the two countries were much friendlier.

The Messenians went in and out of friendship with the Akhaian League. When the Spartans under Kleomenes took Megalopolis in Arkadia, the Messenians took in Philopoimen and his people. They took part in the battle of Sellasia (222 or 221 BC) with the Akhaians and conquered Sparta. The Spartan dictator Nabis conquered Messene, but was driven out by Philopoimen. Later during a conflict with Akhaia, the Messenians captured Philopoimen and a small faction murdered him. After that Messenia was closely bound to the Akhaian League until the Roman conquest, at which point Messenia became just another part of the province of Achaea.