The make-up artist sees the look as "a boybeat", which he previously defined in a chat with Allure as "an androgynous way to look at makeup being masculine and feminine at the same time, adding a bit more structure than you would have naturally".
He also focused on bringing out Beyonce's "inner glow" by using several techniques as well as highlighting products.
When it comes to foundation, Sir John believes people should always apply it on wet, moisturized skin in order to 'lock in' their glow.
The cosmetics expert, who used Marc Jacobs Beauty products for Beyonce's photo shoot, started with the Under(cover) Perfecting Coconut Face Primer to hydrate the star's skin.
He then started working on the star's glow, beginning with the Dew Drops Coconut Gel Highlighter in the Fantasy shade.
Sir John applied to onto the high points of Beyonce's face, which he said is key when using highlighter.
"Always avoid shimmer on the front of the face. Apply it to your angles for sexiness," he said.
Next, Sir John used foundation that was slightly darker than Beyonce's natural skin tone, which he mixed with more of the highlighting drops to add more definition to the singer's face.
"It's all about a glowy contour," he said. "Dew Drops are worth their weight in gold. It's the one thing I have in my bag everywhere — I use it for concerts, for shoots, for tours — I use it religiously."
Sir John then used the brand's Perfecting Coconut Setting Powder to set the make-up and finish off the look.
Beyonce was given full control of Vogue's September issue, in an unprecedented move from the magazine's editor-in-chief Anna Wintour, who usually oversees the making of what has become the most iconic publication of the fashion industry.
The singer chose 23-year-old photographer Tyler Mitchell to take her photos for the magazine.
Tyler, a native of Atlanta, has become the first black photographer to shoot a Vogue cover, as well as one of the youngest to ever land the assignment.
In the magazine, Beyonce explained that giving birth to her twins Rumi and Sir in June 2017 changed the way she viewed her body, and led her to adopt a more natural look.
The twins were born via C-section, and after the major procedure, Beyonce gave herself time to recover.
"During my recovery, I gave myself self-love and self-care, and I embraced being curvier. I accepted what my body wanted to be," she wrote.
"After six months, I started preparing for Coachella. I became vegan temporarily, gave up coffee, alcohol, and all fruit drinks. But I was patient with myself and enjoyed my fuller curves. My kids and husband did, too."
That approach was one of the factors behind her natural make-up look for her Vogue pictures.
"I think it's important for women and men to see and appreciate the beauty in their natural bodies," she added. "That's why I stripped away the wigs and hair extensions and used little make-up for this shoot."
