It first acknowledged the problem with Outlook and Hotmail on Tuesday evening.
"Some users may be receiving excessive spam mail," a service page update stated.
The company later said it had managed to put in place two sets of fixes to protect users' inboxes and its own infrastructure.
Many affected users had complained about the issue on social media.
"Getting a spam/junk email about every minute into my main inbox," tweeted Ben Nelson.
"Drowning in junk mail," added Jennifer Roseblade.
But one Reddit user was able to see a funny side.
"Look at all of these great deals I've been missing out on for years," Peck Ed wrote.
"Now if you chaps will excuse me, I'm off to become a... millionaire getting a great deal on my car insurance with my new Russian bride at the Casino with my free bets."
Microsoft has not disclosed what had caused the issue.