The saga, which is yet to reach a conclusion, enveloped into a high-stakes game of personal attacks just before last year's finals.
Essendon was kicked out of the finals, coach James Hird suspended and the club fined $2 million.
Click here to read our Q&A with the chief
"We're currently reviewing all of that with the Commission," chief executive Andrew Demetriou told AFL.com.au.
He conceded there were elements of the process adopted by the League that did need to be looked at.
AFL won't bailout Swans if Lance Franklin deal backfires
"When you're in the moment you think you're doing everything that you could possibly do. It was a very complex situation," Demetriou said.
"Look, I'm pretty proud of the way the AFL handled the supplements saga and the investigation with ASADA."
Describing the saga as a "wake-up call", Demetriou said the League was now "infinitely better placed" to avoid a repeat of the situation.
The AFL has beefed up its integrity unit to 14 full-time staff and is equipped with a raft of surveillance and IT capabilities.
Demetriou admitted last year "got personal" and said it was preferable that didn't happen again.
"There were lots of things that occurred last year that were beyond your control," he said.
Demetriou said Essendon's decision to provide a lump-sum payment to suspended coach James Hird was beyond his control, but admitted the way that part of the story unfolded wasn't a good look.
"It wasn't a great ending to the year, so we shouldn't pretend otherwise," he said.
"It's a matter entirely for Essendon and James Hird. It's obviously an agreement they've reached between themselves."
Demetriou said the AFL would co-operate fully with former Federal Court judge Garry Downes, appointed by the Federal Government, to try and finally bring an end to the ASADA investigation.
It's hoped a possible end-date will become clearer in the next couple of months.
Twitter: @MattThompson
