Magoffin was elected governor of Kentucky by a vote of 76,187 to 67,283 over Joshua Fry Bell, taking office on August 30, 1859.
He supported states' rights and the institution of slavery.
Although he believed in the right of states to secede from the union, he hoped to avoid this outcome by reaching an agreement between the southern and northern states.
To that end, he wrote a circular letter to the governors of the slave states on December 9, 1860 detailing a plan to save the Union.

Magoffin's plan was to unite the slave states around a set of minimum concessions to see if the North would accept them as an alternative to war.
The concessions included a constitutional amendment repealing any state law that interfered with enforcement of the Fugitive Slave Act, passage of amendments to the Fugitive Slave Act ensuring that any state that would not return a fugitive slave or obstructed a slave's return would compensate the owner of the slave, passage of a law requiring extradition of anyone indicted by a grand jury for enticing the escape of a slave, passage of an amendment to the constitution guaranteeing slavery in all current and future territories south of 36 degrees north latitude, passage of an amendment to the constitution guaranteeing all states the right of using the Mississippi River, and provide protection for southern states in the U.S. Senate from oppressive slavery legislation.
After the slave state governors refused Magoffin's plan, he endorsed the Crittenden Compromise, authored by fellow Kentuckian John J. Crittenden.

In January 1861, Magoffin called the state legislature into special session and asked them to call a convention to determine Kentucky's course in the Civil War.
The Unionist majority in the legislature feared that the vote of the convention would be to take Kentucky out of the Union; consequently, they refused to call the convention.
In response to President Abraham Lincoln's call for troops on April 15, 1861, Magoffin defiantly declared by telegram, "I will send not a man nor a dollar for the wicked purpose of subduing my sister Southern States."
Encouraged by Magoffin's rebuff of Lincoln, Confederate Secretary of War LeRoy Pope Walker requested Kentucky troops for the southern cause a week later, but Magoffin similarly refused him.

Magoffin called another special session of the legislature in May 1861.
Again, the legislators refused to call a convention to determine the state's course in the war.
Instead, they approved a resolution of neutrality, and Magoffin proclaimed this position on May 20, 1861.
Later that month, Magoffin sent a letter to Confederate President Jefferson Davis asking that he recognize and honor Kentucky's neutrality.
In August, he sent an identical letter to President Lincoln.

Although Magoffin pledged "to abide by the will of the majority of the people in the state" and to uphold the state and federal constitutions, Unionists in the legislature did not trust Magoffin.
In the state's special elections in June 1861, Unionist candidates swept nine of Kentucky's ten congressional districts and obtained two-thirds majorities in both houses of the General Assembly.
From then on, they routinely overrode Magoffin's vetoes.

In early September 1861, both federal and Confederate troops entered Kentucky.
Magoffin declared both sides equally guilty of violating Kentucky's neutrality and demanded that both sides withdraw.
A resolution calling for immediate withdrawal by both Union and Confederate forces was defeated in the legislature.
Instead, the legislature passed a resolution ordering only the Confederate troops out of the state.
Magoffin vetoed the resolution, but his veto was overridden, and he obediently issued the order for the Confederates to withdraw.
In November 1861, a self-constituted convention of southern sympathizers met at Russellville, Kentucky in order to form a provisional Confederate government for the state.
Despite his southern sympathies, Magoffin denounced the actions of this convention.

Magoffin and the legislature continued to clash throughout the remainder
Magoffin was elected governor of Kentucky by a vote of 76,187 to 67,283 over Joshua Fry Bell, taking office on August 30, 1859. He supported states' rights and the institution of slavery. Although he believed in the right of states to secede from the union, he hoped to avoid this outcome by reaching an agreement between the southern and northern states. To that end, he wrote a circular letter to the governors of the slave states on December 9, 1860 detailing a plan to save the Union.
Magoffin's plan was to unite the slave states around a set of minimum concessions to see if the North would accept them as an alternative to war. The concessions included a constitutional amendment repealing any state law that interfered with enforcement of the Fugitive Slave Act, passage of amendments to the Fugitive Slave Act ensuring that any state that would not return a fugitive slave or obstructed a slave's return would compensate the owner of the slave, passage of a law requiring extradition of anyone indicted by a grand jury for enticing the escape of a slave, passage of an amendment to the constitution guaranteeing slavery in all current and future territories south of 36 degrees north latitude, passage of an amendment to the constitution guaranteeing all states the right of using the Mississippi River, and provide protection for southern states in the U.S. Senate from oppressive slavery legislation. After the slave state governors refused Magoffin's plan, he endorsed the Crittenden Compromise, authored by fellow Kentuckian John J. Crittenden.
In January 1861, Magoffin called the state legislature into special session and asked them to call a convention to determine Kentucky's course in the Civil War. The Unionist majority in the legislature feared that the vote of the convention would be to take Kentucky out of the Union; consequently, they refused to call the convention. In response to President Abraham Lincoln's call for troops on April 15, 1861, Magoffin defiantly declared by telegram, "I will send not a man nor a dollar for the wicked purpose of subduing my sister Southern States." Encouraged by Magoffin's rebuff of Lincoln, Confederate Secretary of War LeRoy Pope Walker requested Kentucky troops for the southern cause a week later, but Magoffin similarly refused him.
Magoffin called another special session of the legislature in May 1861. Again, the legislators refused to call a convention to determine the state's course in the war. Instead, they approved a resolution of neutrality, and Magoffin proclaimed this position on May 20, 1861. Later that month, Magoffin sent a letter to Confederate President Jefferson Davis asking that he recognize and honor Kentucky's neutrality. In August, he sent an identical letter to President Lincoln.
Although Magoffin pledged "to abide by the will of the majority of the people in the state" and to uphold the state and federal constitutions, Unionists in the legislature did not trust Magoffin. In the state's special elections in June 1861, Unionist candidates swept nine of Kentucky's ten congressional districts and obtained two-thirds majorities in both houses of the General Assembly. From then on, they routinely overrode Magoffin's vetoes.
In early September 1861, both federal and Confederate troops entered Kentucky. Magoffin declared both sides equally guilty of violating Kentucky's neutrality and demanded that both sides withdraw. A resolution calling for immediate withdrawal by both Union and Confederate forces was defeated in the legislature. Instead, the legislature passed a resolution ordering only the Confederate troops out of the state. Magoffin vetoed the resolution, but his veto was overridden, and he obediently issued the order for the Confederates to withdraw. In November 1861, a self-constituted convention of southern sympathizers met at Russellville, Kentucky in order to form a provisional Confederate government for the state. Despite his southern sympathies, Magoffin denounced the actions of this convention.
Magoffin and the legislature continued to clash throughout the remainder
Beriah Magoffin