Her Majesty and Prince William arrived at the Defence Science and Technology Laboratory (Dstl), near Salisbury, on Thursday morning to formally open the new Energetics Analysis Centre.
The Queen has been hunkered down in Sandringham, Norfolk with the Duke of Edinburgh after spending the spring lockdown at Windsor Castle.
The occasion marked the first time she made an appearance outside her protective lockdown bubble since March 9 when she attended the Commonwealth Service at Westminster Abbey.
On March 18, she also had her last audience at Buckingham Palace before the nation was plunged into lockdown.
At Porton Down, the Queen and her grandson have been greeted by the Chief Executive, Mr Gary Aitkenhead.
They are taking a private tour of the Energetics Enclosure to look at displays of weaponry and tactics used in counter intelligence.
Next, the pair will the Energetics Analysis Centre to view a demonstration of a Forensic Explosives Investigation and meet staff employed in Counter Terrorism and Security.
The Queen and Prince William are to meet Dstl staff involved in identifying the nerve agent and subsequent clear up of the Novichok incident of 2018 as well as members of the military who were also directly involved in the response.
They also greeted scientists, working in analytic research to provide vital support to the UK’s Covid response.
In recognition of their work, the Duke will present the Firmin Sword of Peace to representatives of 102 Logistic Brigade.
Before leaving, the Queen will also formally open the new Energetics Analysis Centre and unveil a plaque.
The Queen arrived separately from William.
Heightened safety precautions were taken ahead of the visit to protect the monarch against coronavirus.
All 48 people who were due to come into close contact with the monarch and the duke were tested for Covid-19 by the Dstl.
Small groups of those taking part in the royal visit were arranged two metres apart to ensure social distancing.
The Queen arrived by helicopter and William by car.
They last saw each other face to face when they met privately at Balmoral during the summer.
William last accompanied his grandmother on an external public engagement in July 2017, when they met members of the community affected by the Grenfell Tower fire.