The losses will come as no surprise to many fashion experts as the sector has taken a massive hit due to the credit crunch.
However, due to the high profile of Bono and his wife, many thought Edun would not suffer as much as other companies.
Accounts filed for the business reveal that the fashion company retained losses of $19m (€12.8m) in 2008, a 23pc increase from the previous year's $14.5 (€9.7m).
Edun, which was set up in 2005, sells organic cotton wares that are made in countries such as Kenya, Peru and India.
Sales to Edun Americas, its New York-based subsidiary, fell from $3.2m (€2.1m) in 2007 to $1.6m (€1m) last year.
Earlier this year, Edun sold almost 50pc of the business to French luxury goods firm LVMH for $8.5m (€6m).
The company behind brands such as Louis Vuitton, Dom Perignon champagne and Givenchy said that its investment in Edun "demonstrates that it's possible to promote fair trade in the fashion industry".
Listed on the Paris stock exchange, it has a market capitalisation of more than $40bn (€29bn).
The U2 frontman Bono and his wife created the brand four years ago and other shareholders include Bono's brother Norman Hewson.
Before the brand was launched, Ali organised charity fashion shows in Ireland when she brought over supermodels Naomi Campbell and Helena Christensen.
"Bono and I wanted to trade on the ground with the government, to put our money where our mouth is, and find out how easy or difficulty it was," Ali explained.
"It was a huge learning curve as I have no experience at all. It's just basic common sense, and the rest is obstacles."
And in August of this year, the company was embroiled in a controversy with fashion designer Stella McCartney.
Nude, the natural skincare company Ali created with Fresh & Wild founder Bryan Meehan, considered Stella McCartney's perfume Stella Nude to be an infringement of their trademark and took the case to court.
In August the High Court ruled that Nude skincare had a clearly arguable claim of trademark infringement and the case was set for the new year.
"It's an interesting time, and a new process, and it's the desire of the manufacturers to change that is the important thing," Ali said about the ethical clothing line.