Born in Chittagong, Bangladesh, Chowdhury received his undergraduate degree in Aeronautical Engineering from the Indian Institutes of Technology (IIT) in Kharagpur, India (from which he received the Distinguished Alumnus Award) and a graduate degree in Industrial Management from Central Michigan University, Mt. Pleasant, Michigan where he also received the Distinguished Alumnus Award. He came to the United States 1991 and eventually settled in Bloomfield Hills, Michigan. Chowdhury became a naturalized citizen in 2004.

In 1996, Chowdhury co-authored with Ken Zimmer a book titled QS-9000 Pioneers. The book was an early effort to demonstrate how companies "revitalized" their Manufacturing practices with standardized quality management processes. According to the book jacket, the book was endorsed by quality management experts Dr. Armand Fiegenbaum, Philip B. Crosby, J.D. Power III, and Dr. Genichi Taguchi.

Joining American Supplier Institute in 1997, Chowdhury began to work with his mentor Dr. Genichi Taguchi, developer of robust engineering theory, and Taguchi's son, Shin Taguchi who is also an Engineer. Together, they co-authored a book titled Robust Engineering (2000) that was designed to help producers bring products to market at a faster rate and at lower cost, and yet maintain a high level of quality.

Inspired by a book titled The Leader of the Future, Chowdhury began collaborating with other management thinkers to analyze leadership and organizational development. Management 21C was published in 2000 with contributions from Peter Senge, C K Prahalad, James Kouzes, Barry Z. Posner, Sumantra Ghoshall, Christopher A. Bartlett, and Rosabeth Moss Kanter.

The Six Sigma quality movement was reaching its height in popularity in 2001 when Chowdhury wrote his next book, The Power of Six Sigma. Reported as a bestselling nonfiction book, some reviewers noted that Chowdhury made complex topics quality management issues easy to understand by using a fictionalized story to model important concepts.

In 2002, Chowdhury wrote two more books on Six Sigma. Design for Six Sigma helped draw attention to emerging DFSS methodology that simplifies an otherwise complex management theory. The follow-up book The Power of Design for Six Sigma, stood out because unlike other books on the topic, Chowdhury successfully engaged a broad audience that included assembly line workers and CEOs to make Six Sigma even more accessible. These books lead Chowdhury to create a management implementation system he called “LEO” (Listen-Enrich-Optimize). This concept was later highlighted his book The Ice Cream Maker (2005) and later expanded in The Power of LEO (2011). His latest book is "Robust Optimization" (2016) co-authored with Shin Taguchi.

In 2003, Chowdhury formed ASI Consulting Group, LLC and became its Chairman and CEO.

The Ice Cream Maker (2005) continues to sell well and receive positive reader reviews.

In 2009, the Conference Board Review described Chowdhury as "an excitable, enthusiastic evangelist for quality." In an article speculating about an up-and-coming book by Jack Welch, the New York Times described Chowdhury as a "leading Quality Expert". Marshall Goldsmith called Chowdhury "the Quality Prophet" in an interview published by Business Week in 2007.

In 2011, the Society of Automotive Engineers (SAE) established the “Subir Chowdhury Medal of Quality Leadership” to be given each year to a global leader who promotes Quality in mobility industry.

In 2013, Thinkers 50 again recognized Chowdhury with a nomination for the 2013 "Breakthrough Idea" award for his work on "Economics of Quality".

The Subir and Malini Chowdhury Center for Bangladesh Studies was established at University of California, Berkeley, January 2014. The Center’s mission is to the build ties between institutions in Bangladesh and the University of California. It will also will conduct research, promote art and culture, and offer three scholarships, namely: The Subir Chowdhury Fellowship on Quality of Life in Bangladesh for graduate students; The Malini Chowdhury Fellowship on Bangladesh Studies for graduate students in any field that concentrates on Bangladesh studies; and The Subir Chowdhury Undergraduate Scholarship awarded to students concentrating in South and Southeast Asian Studies at Berkeley with matching awards from the Ford Challenge, a fund provided by a Berkeley donor to match undergraduate scholarship gifts.

In 2017, Chowdhury published his 15th book titled The Difference: When Good Enough Isn't Enough.

Chowdhury started his career as a quality and systems Engineer assigned to General Motor’s Delphi Division in 1993. From 1998-2003 Chowdhury worked as an Executive Vice President of the American Supplier Institute, which at the time was a provider of technical training for mostly Automotive Manufacturing companies in the U.S.