After an exhaustive search, we have finally found the culprit:
Meet John "The Donut Thief" Smith, a notorious serial donut eater.
His modus operandi:
Security footage:

Multiple witnesses place John at the scene of the crime.
"I swear, I didn't eat it!" - John Smith
"He's always eating the last donut!" - Karen, Intern
We recommend keeping a closer eye on the break room fridge.
We also suggest investing in a donut-proof box.