Bluefields was hit with extreme impact. Almost all of the 7,500 structures in the city were demolished or had their roofs blown off. The majority of the main buildings in the city were destroyed. The hurricane also wreaked havoc on agriculture in the country. Around 15,700 head of cattle, 20,000 pigs, and 456,000 chickens were killed. The hurricane also caused severe disruption in most of Nicaragua's remaining rain forests in the areas it hit, and also stripped trees of leaves. Hurricane Joan caused transportation difficulties in the country. Floodwaters destroyed 30 bridges and seriously damaged 36 others. Roads totaling 404 miles (650 km) in length were washed away.
In an unfortunate coincidence, Hurricane Joan hit shortly after an armed conflict in the region had started to cool off. The hurricane destroyed much of the infrastructure in Nicaragua, contributing to a recession that was already underway. The losses to cash crops severely reduced exports to under 200 million dollars (1988 USD). These factors combined to aggravate a recession and deepen the economic crisis. Government spending to rebuild infrastructure negated recently-introduced anti-inflation measures. Hurricane Joan was a partial cause of Nicaraguans being, on average, worse-off than they were in the 1970s. In all, the storm left at least 250,000 people homeless.