The Church Protection Act would allow individual places of worship to decide whether to allow concealed handguns and who could carry them. Churches that take no action will remain off-limits to guns.
The Republican-controlled House passed the bill 85-8 with bipartisan support last week. The measure previously passed the Republican-controlled Senate 28-4.
The law takes place immediately.
Gun advocates praised Beebe for his action.
"It is crucial to protecting the freedom of religion and property rights," said Nicholas Stehle, a member of the board of directors of the advocacy group Arkansas Carry.
"The state has no business meddling in the affairs of our churches," Stehle said.
Arkansas joins a handful of other states, including South Carolina, Wyoming and Louisiana, that allow guns in churches, according to the National Conference of State Legislatures.