The moves included several critical junctions in which Gates requested a larger share of the company and Allen granted it, The Wall Street Journal reported Wednesday.
The Journal said it reviewed an advanced copy of Allen's autobiography, "Idea Man: A Memoir of the Co-Founder of Microsoft," expected to hit bookstore shelves April 17.
The book says Gates requested a 60-40 split in the partnership in the early 1970s, when the two dropped out of college and started the business in New Mexico.
Gates based his reasoning on his share of the work on early operating systems, and Allen agreed to the split.
Later Allen's share was whittled down to 36 percent, but when Allen asked for a larger share based on his work developing SoftCard, Gates refused.
"In that moment, something died for me," the book says. "I'd thought that our partnership was based on fairness, but now I saws that Bill's self-interest overrode all other considerations."
The book also says Allen overheard Gates and executive Steve Ballmer discuss reducing Allen's shares after he was treated for cancer in 1982.
Allen confronted the two and they abandoned their plan, the book says.
"My partner and my colleague were scheming to rip me off. It was mercenary opportunism, plain and simple," the book declares.
Gates is thanked in the introduction to the book and the co-founders -- both billionaires several times over -- are cordial, the Journal said.
In the book, Allen says Gates was "everything you'd want from a friend, caring and concerned," when he was undergoing chemotherapy two years ago for non-Hodgkin's lymphoma.
In a statement, Gates said, "While my recollection of many of these events may differ from Paul's, I value his friendship and the important contributions he made to the world of technology and at Microsoft."