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Building up to the Spanish-American war the port of Fernandina was used as a base of operation for those sympathetic to the Cuban plight. Arms, ammunition, and recruits were shipped from her port to Cuba. Once War was declared Fort Clinch was prepared for up to 10,000 soldiers and the economy of Fernandina began to grow again. But it was short lived as additional railroads built out in the early 20th Century to cities like Jacksonville and Savannah. Finally, in the late 1930s, the mills arrived in Fernandina and released the citizens of the community from their reliance on cotton and tobacco to timber and industry.

Fort Clinch was an immediate target of acquisition for the Union during the Civil War. The Union Navy arrived on 2 March 1862 firing cannon volleys at the last two retreating railroad ships of citizens from evacuated Fernandina. As in most wars, not all citizens evacuated, and those left behind found themselves in an occupied territory once again, with limited freedom. But freedom did come to the black slaves of Fernandina which far outnumbered their white owners. And when the reconstruction period began after the War it was the "black" county of Nassau which rose to power in the government offices of Nassau County, while the white citizens still held the land and controlled the jobs. It was this inimical system that led to the strikes in the 1880s by the black workers until again the Yellow Fever broke out and all citizens were to busy nursing, to think of other troubles.