When he took over from Steve Ballmer in 2014, Nadella took home $84.3 million which is the highest earnings in a fiscal year for him so far.
"For fiscal year 2019, the annual total compensation for the median employee of the Company (other than our CEO) was $172,512," the company said.
"The past fiscal year offered another record year for financial performance, and Microsoft delivered strong results for our shareholders, including a return of $30.9 billion in the form of share repurchases and dividends," wrote the board of directors.
During the first five-year performance period, Microsoft's market capitalisation increased $509 billion (from $302 billion to $811 billion).
"Microsoft's relative TSR was in the 97th percentile, resulting in Nadella earning and vesting in the maximum 900,000 shares," the company said in the filing.
Microsoft's board of directors last month authorized another $40 billion in share repurchases and raised its quarterly dividend by 5 cents or 11 per cent to 51 cents a share.
The company bought back $19.54 billion in shares last year. In the previous fiscal year, the buybacks was worth $10.72 billion - all under Nadella's tenure.
"The new share repurchase programme, which has no expiration date, may be terminated at any time. The dividend is payable on December 12 to shareholders of record on November 21, 2019. The ex-dividend date will be November 20, 2019," the company said in a statement.
The company will hold its annual shareholders meeting on December 4.
This year's annual shareholders meeting will be held virtually and hosted by Nadella, Amy Hood, chief financial officer, Brad Smith, President and chief legal officer and John W. Thompson, Microsoft independent board chair.
Driven by growth in its Cloud and Surface laptop segments, Microsoft posted revenue of $33.7 billion and net income of $13.2 billion for its fourth quarter that ended on June 30.
For its entire fiscal year 2019, Microsoft reported revenue of $125.8 billion which increased 14 per cent and $39.2 billion net income - setting a new record fiscal year for the company.
Microsoft that continues to be valued as a $1 trillion company returned $7.7 billion to shareholders in the form of share repurchases and dividends in the fourth quarter of fiscal year 2019.