Zubbles were invented by Tim Kehoe, a toy creator from St. Paul, Minnesota. After an unexplained breakthrough in his kitchen, he was able to produce blue bubbles, that, unsuitably for a toy, stained clothing. After an eight-year-long delay in developing the idea further, he recommenced his investigations after forming a new toy company. 
In the process of trying to rediscover the recipe, he changed the formula, making the coloring water-soluble. However, having to wash off the color from the bubbles rendered them unsuited to a mass-market toy. Kehoe hired the dye chemist Ram Sabnis, who arrived at a formula where the color would disappear on its own, with sufficient exposure to air, and without washing or staining.
The company entered into a global license agreement with Spin Master Ltd. for Zubbles Colored Bubbles in December 2005.  Despite announcements of expected release dates, Spin Master dropped plans for commercial production due to complexities in the manufacturing process.
In 2008, the company reached a licensing agreement with a new toy company called Jamm Company. Zubbles commenced commercial sales in June 2009.
In 2011, Crayola disputed the patent given to Kehoe/C2C Technologies in a lawsuit which claimed that colored bubbles should be in the public domain.
Kehoe died unexpectedly at the age of 43 in 2014.