Alexander (bishop, 1123–48) rebuilt and expanded the cathedral, but it was mostly destroyed by an earthquake about forty years later, in 1185 (dated by the British Geological Survey as occurring 15 April 1185). The earthquake was one of the largest felt in the UK: it has an estimated magnitude of over 5.

The primary collapse of the Lincoln Cathedral’s famous central spire occurred in 1549 due to a combination of architectural ambition, structural decay, and a severe storm. At the time, the spire was a massive timber structure encased in lead, reaching an estimated height of 525 feet, which made it the tallest building in the world (surpassing the Great Pyramid of Giza). Over centuries, the heavy lead casing trapped moisture, leading to the "rotting" of the wooden support beams beneath it. This weakened the connection between the heavy spire and the masonry tower. During a particularly violent storm in 1549, high winds put immense lateral pressure on the weakened structure, causing the entire spire to topple. It was never rebuilt, which is why the cathedral today has a "flat-topped" central tower. Earlier in its history, in 1237, the original central tower also collapsed—that time it was due to poor foundations and the "experimental" nature of early Gothic architecture, which pushed stone to its limits without a full understanding of weight distribution. The 1549 collapse, however, remains the most famous, as it ended the cathedral's 238-year reign as the tallest structure on Earth.