Michael Green, 62, began his 40-minute protest after staff refused to serve him in the drive-through lane of a Skegness branch on 1 August.
At Skegness Magistrates' Court, he denied being drunk in charge of a carriage under the 1872 Licensing Act.
Prosecutors said there was no public interest in continuing the case.
The court heard staff at the fast food chain had refused to serve him "for insurance, and health and safety reasons".
A security guard photographed the former HGV driver, who is registered disabled after a head injury in 1997, talking to a police officer who attended the scene with a breathalyser.
Mr Green, of Clifford Road, Skegness, refused to give a breath specimen. He insisted he was not drunk and that his vehicle was roadworthy, the court heard.
The Crown Prosecution Service (CPS) said: "We do not believe it is in the public interest to prosecute Mr Green.
"It may be he was part of some form of disturbance at McDonald's on the day in question, but we do not believe it amounted to any criminal offence."
In a statement, McDonald's said it "supported the decision taken by our colleagues based on the risks deemed to be present".
"It was felt in this instance that it was not safe for the operator of the mobility scooter to be in the drive-through area," the company said.
The 1872 licensing act was originally brought in to crack down on anyone caught drunk in charge of a carriage, steam engine, bicycle, a horse or a cow.
Mobility scooters are classed as invalid carriages.
A man accused of being drunk on a mobility scooter while staging a sit-in at a McDonald's drive-through has had the case against him dropped.