Prince Andrew left the Navy in July after 22 years service
Prince Andrew, who started his new role as Special Representative for International Trade on Monday, visited the Halewood home of Jaguar Cars on Thursday.
On Wednesday evening the Duke was staying at nearby Knowsley Hall when a gamekeeper was shot in the grounds.
A Scotland Yard spokeswoman confirmed the Duke had been staying at the Merseyside Estate but said he had not been in any danger.
First visit
The whistlestop tour of the Jaguar plant was the Duke's first visit to the north-west since starting his new role.
He left the Royal Navy in July after 22 years of service.
Dressed in a grey striped suit, pale blue shirt and Navy tie, the Duke toured the Halewood plant as part of a fact-finding trip.
He spent more than 90 minutes touring the assembly line where he chatted to workers on the shop floor.
After signing the visitor's book, the Duke left for the Partnership for Learning centre, in Liverpool.
He then visited Liverpool-based Powder Systems Ltd, which manufactures and exports pharmaceutical processing equipment.
His final appointment was at the international business centre, in Warrington, Cheshire.
The Duke stayed overnight at the Knowsley Hall Estate as a guest of the Earl of Derby.
Recent incidents
At 2310 BST on Wednesday, a 38-year-old gamekeeper was shot in the arm when he went to investigate noises in kennels near the perimeter fence.
Detectives from Merseyside police said the shooting followed a number of recent incidents involving poachers at the Estate.
The spokeswoman for Scotland Yard said: "The Duke of York was present but his safety and security was not compromised."
The gamekeeper was released from hospital after treatment.