After the humiliation of the first siege's failure in December 1822, the Ottoman command reorganized its approach to western Greece. Mustafa Pasha of Scutari led a new expedition, marching through Trikala to Karpenisi in the summer of 1823. The Greeks attempted to stop him at Karpenisi, and the engagement became the Battle of Karpenisi — a costly fight for both sides. The Albanians under Mustafa suffered around 1,000 casualties. But the Greeks lost something harder to replace than numbers: Markos Botsaris, one of their most capable commanders, was killed in that battle. A hero of the first siege and a symbol of Greek resistance in western Greece, his death was a blow to the defending forces that went beyond the tactical. A second Greek attempt to halt the Ottoman advance, at Mount Kaliakouda on 29 August 1823, resulted in 200 Greek casualties without stopping Mustafa's march.

On 17 September 1823, Omer Vrioni — who had commanded the first siege a year earlier and failed — arrived with his troops and joined forces with Mustafa Pasha. The combined army was now substantially larger and included Albanian troops under both commanders. They settled on a coordinated plan: besiege both Missolonghi itself and the island of Aitoliko, which sat in the lagoon and controlled the water approaches to the town. Without Aitoliko, supplies by sea could not reach Missolonghi. The siege of Missolonghi began on 20 September 1823, opened by a bombardment of Aitoliko. Thousands of cannonballs were fired at the island. Only a few found their targets. The assault on Aitoliko failed. Inside the Ottoman camp, matters then deteriorated in a different direction entirely: clashes broke out between Gheg Albanian and Mirdite Albanian soldiers over the shortage of food. An army that could not feed itself could not sustain a siege.

The combination of factors that ended the second siege was familiar to anyone who had studied the first. The autumn campaign meant the onset of winter, which the marshy terrain around Missolonghi made especially punishing for a besieging force. Disease spread through the Ottoman camp, as it had in 1822. The simultaneous Ottoman military operations in eastern Greece were failing, reducing pressure on the Greek defenders elsewhere and allowing some Greek forces to threaten the besiegers from the rear. Greek attacks on foraging parties — small engagements that do not appear in the main histories but degraded Ottoman supply chains steadily — added to the cumulative pressure. By 17 November 1823, the Ottoman commanders abandoned the siege. Missolonghi was still in Greek hands.

The aftermath of the second siege carries a particular weight in hindsight. Missolonghi had now twice repelled Ottoman assault. Lord Byron arrived in the town in January 1824, drawn by the cause of Greek independence and by the town's reputation as a center of resistance. He died there of fever on 19 April 1824. His death, and the global attention it brought, became part of the town's identity. Then, in April 1825, the third siege began — far larger, longer, and more devastating than either of the first two. The third siege would last nearly a year, end in the Exodus of April 1826, and result in the town's fall and the deaths of many of its people. The second siege, in this light, belongs to the years when Missolonghi held — the years before the city's luck finally ran out.

All three sieges of Missolonghi were shaped by the same geography: the lagoon to the north of the town, the Gulf of Patras to the south, the marshy terrain on all landward approaches. The island of Aitoliko, which the second siege specifically targeted, sits in the center of that lagoon, controlling the water lanes that were Missolonghi's only reliable supply route. No siege commander could ignore it, and yet every siege commander found it extraordinarily difficult to take. The second siege's failure at Aitoliko was not an accident or a fluke — it was the lagoon asserting its utility again. The site lies at 38.447°N, 21.369°E, north and slightly east of Missolonghi proper, in terrain that still floods seasonally and still resists straightforward movement across it.