The city's Department of Health heads to court to fight the March ruling that blocked the ban on the sale of sugary drinks larger than 16 ounces.
A judge called the law arbitrary and beyond the board of health's authority one day before it was set to take effect.
Bloomberg says the measure is important for public health.
"The loopholes in this rule effectively defeat the stated purpose of this rule," Judge Milton Tingling wrote in his ruling, which was seen as a victory for the beverage industry, restaurants and other business groups that called the ban unfair.
Said American Beverage Association spokesman Christopher Gindlesperger, referring to the initial decision overturning the ban, "We feel the justice's decision was strong and we're confident in the ruling."
The city says other organizations had filed legal briefs in support of the city's appeal. Those organizations include the National Alliance for Hispanic Health and the National Association of Local Boards of Health, as well as 30 others.
Bloomberg has made public health a cornerstone of his administration, from requiring calorie counts to be posted on menus and barring trans fats in restaurant foods.