US authorities stated that 34-year-old Matthew Michael Robinson had been arrested and charged with three counts of criminal mischief on Wednesday.
He was further released on bail on Thursday.
Other LGBTQ+ murals alongside the artwork of deceased journalist Ms McKee were also defaced.
They were outside LGBTQ+ support groups, The Center and Zebra Youth, and had been daubed with racist and homophobic graffiti.
One of the murals paid tribute to the 49 victims of the devastating 2016 Pulse nightclub shooting.
Ms McKee visited the city in 2017 as part of an international exchange programme in the wake of that mass attack.
She dedicated a TED talk at Stormont to the victims of the shooting and all LGBT people who died by suicide.
A swastika, anti-LGBT and anti-trans messages were painted on Ms McKee’s memorial, which was erected in 2019 and bears an image of the late 29-year-old set against a rainbow-coloured heart.
Ms McKee was shot dead by a New IRA gunman while observing rioting in the Creggan area of Derry in April 2019.
Her mural was erected after the City of Orlando passed a motion to honour her in the aftermath of her murder.
Zebra Youth said the graffiti was a work of a “hate group”.
It added volunteers had since removed the message.
A statement from Orlando Police Department reads: “On August 26, 2023 at approximately 3.20am , officers responded to 927 and 946 North Mills Avenue in reference to several murals that were defaced on buildings utilized for LGBTQ+ outreach. The graffiti included hateful rhetoric targeting the LGBTQ+ community.
“On September 13, 2023, Matthew Michael Robinson was arrested and charged with 3 counts of Criminal Mischief.
“We will be seeking enhancements for evidence of prejudice during the commission of these crimes.”
Florida politician Anna Eskamani said: “Lyra has a very special place in the hearts of Orlandoans.
“Following the 2016 Pulse nightclub shooting, Lyra not only recognised the tragedy of what happened at Pulse, but she shared her personal experiences as a LGBTQ+ person, talking about Pulse during a 2017 TED Talk that inspired and comforted so many of us.
“We are proud to have a mural dedicated to her in our city, and when it was vandalised this past weekend with Nazi graffiti, our community stepped up immediately to remove the hate speech and restore the mural.
“Lyra serves as a reminder for us to love ourselves, care for our community and to find power in pain.”
Ms McKee’s sister Nichola Corner said she was shocked the memorial had been targeted and thanked those in Orlando for removing the Nazi graffiti from it.
“In this day and age, LGBT people should not have to put up with this,” she added.
“Lyra visited Orlando a year after the nightclub shooting, and it had a profound impact on her.
“She said she felt freer in Orlando than she did here and would love to live there some day.
“She also visited a mosque and spoke to those who helped people in the wake of the shooting.
“This informed a big part of Lyra’s TED talk.
“After Lyra was murdered, the people of Orlando rallied around and a resolution was passed to make Lyra’s birthday an annual day of celebration in the city.
“We were extremely honoured and touched by that.
“We are also touched at how people came out after the murals were targeted and restored them so quickly. It means so much.
“That says everything you need to know about the vast majority of the people of Orlando.
“Those responsible for the graffiti have nothing to offer society. They would be better spending the time having difficult conversations with those they disagree with. They would realise that we are all the same.”