In 1861, the Civil War began and the lighthouse was thrown right in the middle. When Florida seceded to the Union, Confederate soldiers took the lighthouse, along with Forts Barrancas and McRee, while Union soldiers held Fort Pickens on Pensacola Beach. After more than a year of staring across the bay and intermittently exchanging fire with one another, the Confederate soldiers evacuated, and the lighthouse fell under Union control. Unfortunately, the lighthouse didn't make it out of the fray unscathed. Several rounds fired from Fort Pickens had done quite a number on the building. Thankfully, none of the rounds penetrated the outer wall, so the lighthouse was still sound and in working order.
If a war weren't enough to take the lighthouse down, a little natural disaster certainly couldn't do it either. A few years after the end of the Civil War, the lighthouse was struck by lightning, twice, melting some of the metal fixtures inside. Then it had to ride out an earthquake, of all things.