The border has been a prominent feature of the Kent garden for many years and is inspired by the colours of the Sidney Flag, the herald of the owner Viscount De L'Isle.
But over the years its original design statement had been watered down with other colours.
Head gardener Cory Furness said: "The mixed display had moved away from its original concept after a combination of plant reversion, out of place self-seeded displays and poor performing varieties.
"We have taken the border back to, as strict as possible, a blue and yellow concept and removed the oranges, reds and even pinks from the border.
"We have also removed the over dominant shrub displays and gone for a more herbaceous concept, with a few sub-shrubs added into the mix. The plant choice should provide a long season of colour, and a mixture of heights and textures."
The border is due to reopen to visitors on 4 June during Glorious Gardens Week.
Furness and his team has also finished the first phase of a redevelopment and rejuvenation of the rose garden and has around 20 different varieties of pear to be trained onto the walls surrounding the formal garden.
They are a mixture of historic varieties, including a graft of the 13th century Warden pear from Shuttlesworth College in Bedfordshire, 16th century Black Worcester and 17th century Jargonelle, as well as modern varieties like Beth and Concord.
Furness said Penshurst Place had seen a rise in visitor numbers over the past two years as people made several return visits to see changes in the garden and responsed to visitor offers.
"We have been improving the garden year-on-year, with a number of different projects and developments, some minor changes, and some major and as the garden had gone slightly beyond its maturity, visitors are responding to the changes we are making by returning year-on-year to see the changes take place," he said.
"We have also improved our ticketing systems and offers to make becoming a season ticket holder or family season ticket holder more appealing and good value for money."
Seasonal trails around the garden added extras in the activity room and half-term entertainment have also helped, Furness added.