She received a lethal injection at a prison in Terre Haute, Indiana, after a last-minute stay of execution was lifted by the US Supreme Court.
The case attracted attention because her lawyers argued she was mentally ill and suffered serious abuse as a child.
The 52-year-old strangled a pregnant woman before cutting out and kidnapping her baby in Missouri in 2004.
Her victim, 23-year-old Bobbie Jo Stinnett, bled to death.
Montgomery is the first female federal inmate to be put to death by the US government in 67 years.
According to witnesses, a woman standing next to Montgomery during the execution process, removed the inmate’s face mask and asked her if she had any last words. Montgomery responded “no”, and said nothing else.
She was pronounced dead at 01:31 (06:31 GMT). Montgomery’s lawyer, Kelley Henry, said that everyone who had participated in the execution “should feel shame”.
“The government stopped at nothing in its zeal to kill this damaged and delusional woman,” she said in a statement. “Lisa Montgomery’s execution was far from justice.”
The latest execution was postponed twice – first by Covid-19, then by a judge – until a Supreme Court ruling cleared the way for it to take place in the early hours of Wednesday.
In a dramatic move late on Monday, a judge in Indiana had halted the scheduled injection until a mental competency hearing could be held.
Her lawyers argued that she had been born brain-damaged and was too mentally ill to be executed.
As a child she was routinely sexually and physically abused by her father and trafficked by her mother, family members said. Her treatment was so violent that it amounted to torture, her lawyers say.
Her defence team believe that at the time of her crime, Montgomery was psychotic and out of touch with reality. That opinion is supported by 41 current and former lawyers as well as human rights groups like the Inter-American Commission on Human Rights.
But her victim’s family and friends say the murder committed by Montgomery was so horrific that she deserved to be put to death regardless of her mental health.
She killed 23-year-old Stinnett in Skidmore, Missouri, after befriending the pregnant woman online over a shared love of dogs. After driving to Stinnett’s house, Montgomery overpowered the pregnant woman, strangled her with a piece of rope, and cut the baby out of her womb.
Police found Montgomery cradling a new-born girl she claimed to have given birth to the day before. After her story fell apart, she confessed to the killing.
She was found guilty of the crime in 2007. The next day, she was sentenced to death.