The logo and design elements will be used in print material, the new website and signage for the Castlefield bar.
Johnson forged his reputation in the 1980s and 1990s, during the ‘Madchester’ music scene.
He created designs for the Hacienda nightclub and its owners Factory Records, as well as Dry Bar and Barca.
Salford-born Johnson, design director at Havas Lynx, said: “It was a great pleasure to be asked back to play a key part in the branding of Dukes for the next quarter of a century.
“I have lots of very happy memories of Dukes from the last couple of decades or so and it’s great to be involved in its future.
“From my meetings with the architects and client the diamond shape kept cropping up continuously in references for the new interior.
“I wanted the graphics to have a visual connection with the physical space, so it seemed natural to incorporate this as a key element of the new identity.
“We have not lost the Duke of Bridgewater’s head completely and it will appear as part of the wider branding as a nod to the original design.
“We needed a brand that’s fit for 21st century communication and not influenced by quirky fashion or style to take us through the next 25 years.
“It needs to be versatile, neutral and able to work visually across a wide variety of traditional and digital platforms.”
Heaton Moor-based design agency AHOY has created the bar’s new website.