Beta lost some punch before making landfall early on Sunday, and a late turn to the south spared the port of Puerto Cabezas from a direct hit.
Once over land, it lost further steam but was still a strong Category 1 hurricane with winds of 150kph.
Emergency officials said no deaths were reported, although Beta was expected to cut straight across Nicaragua, raising fears of flooding and lethal mudslides in mountain villages.
"We have not had reports of deaths, no people knocked about, nor injured," said civil defence operations chief Samuel Perez. "But we expect rivers to swell."
In the normally sleepy fishing town of Puerto Cabezas in the remote jungle of northeast Nicaragua, residents and Miskito Indian evacuees from fishing villages rushed to makeshift shelters, but Beta caused little structural damage.
In neighbouring Honduras, communications went down as isolated coastal villages flooded, aid officials said.
Both countries were ravaged in 1998 by Hurricane Mitch, whose heavy rains killed about 10,000 people across Central America.
Hurricane Stan killed up to 2000
people in Central America
This month, Hurricane Stan killed up to 2000 people in Central America, most of them Maya Indians in Guatemala whose homes were swallowed in landslides.
About 200 people crammed into one crumbling school in Puerto Cabezas with a rotting wooden frame and holes in its tin roof.
"We had a very bad night. The water leaked in, the children were cold. They brought us here without telling us anything. We don't have food or water," said Norma Smith, a mother of six.
Eight families, including three pregnant women, spent the night holed up in a small Baptist church, its windows protected from howling winds and torrential rain by wooden boards.
"We prayed," said Azucena Coulson, the wife of the pastor, who was on a visit to the United States. "I was the one who was panicking, but I had to keep calm as the church leader."
Beta is the 13th hurricane and 23rd named storm of the relentless, record-breaking Atlantic storm season.
Beta is the 13th hurricane of the
Atlantic storm season
Small fishing hamlets dot the isolated Caribbean coast of Nicaragua and Honduras, populated by Miskito Indians and the descendants of escaped African slaves.
The US National Hurricane Centre warned rains of 25cm to 38cm would hit Nicaragua and eastern Honduras, with isolated maximum amounts of 64cm possible.
"Beta is expected to rapidly weaken during the day today," the Miami-based centre said, with wind speed expected to fall.
Last week, Hurricane Wilma wrecked Mexico's Caribbean beach resorts, flooding Cuba and pounding southern Florida.