The story of this church is really the story of a community on the move. Between the ninth and tenth centuries, the inhabitants of ancient Elymnion built their first parish church on the hill called Panagia, north of present-day Limni, dedicating it to the Nativity of the Virgin. They worshipped there until the sixteenth century. Then, as Ottoman authorities allowed populations to relocate, the people came down from the hills of Kastrias and Panagia to settle permanently on the coast where Limni now stands. They built a new parish church on the very spot the present one occupies, and clustered their first houses around it. The church did not simply serve the town; it anchored it, the fixed point around which a community gathered and grew.

The Greek War of Independence reached Limni with brutal force. In July 1823 the church was destroyed and the town devastated by Yusuf Berkoftsali Pasha's invasion of northern Euboea. Then the tide of history turned. The London Protocol of 1830 established the first independent Greek state, with Euboea inside its borders, and the people of Limni began returning home. Around 1832 and 1833 they threw up a small, rough temple on the ruins, but by 1837 it was judged unfit for a town now growing fast on shipping and farming. On 31 March 1837 the municipal council resolved to build a proper church on the old foundations, sized to match a swelling population, and funded entirely by the townspeople themselves.

The new church reveals who held power in Limni as the modern town took shape. First to step forward with money were the captains and ship owners, making their debut in the town's social life as an organized professional class, the men whose vessels were turning a recovering coastal village into a maritime center. By 1840 they were financing the work through rented pastures, granted plots of land, and the lease of the community house, funneling the income toward completion. The project was finished at the end of 1841. Set on its rock above the harbor, 295 square meters of stone with a courtyard on two levels joined by a stair, the church stands as a record of the people who paid for it, the sailors who built a sanctuary out of their own prosperity and grief.

Inside, the church guards relics and documents that fold centuries into a single room. A silver reliquary holds fragments associated with Saint Nicholas, Saint Barbara, and Saint Mamas, and a hand-shaped reliquary keeps parts said to belong to Saint Minas. There is a pillow reported to come from the chariot of Saint Christodoulos on Patmos. In wooden showcases along the aisles rest older marvels still: a handwritten, leather-bound music book from 1746, a Holy Gospel from 1754, a cloth antimensium dated 1871, and a Russian epitaph from the close of the nineteenth century. Recognized as a monument of modern Greek ecclesiastical architecture and granted special state protection, the church is as much an archive of devotion as a place of worship, every object a thread back into the long memory of Limni.