TDA is associated with certifying factory farms, particularly the mega-dairy Natural Prairie. Both TDA and Natural Prairie have been accused of non-compliance with the organic standards.

Freedom of Information Act disclosures show that TDA has had multiple, serious non-compliances in years past. These non-compliances included not conducting the annual inspections approximately 22% of their clients one year, not having sufficient certification review personnel to comply with and implement the organic certification program, and not conducting unannounced inspections. Overall, TDA has a history of non-compliances coupled with certifying some of the most egregious factory farms.

Although TDA does not certify them all there are just six certified organic dairies in the entire state of Texas. Those industrial-scale operations, according to the most recent USDA data, produce 1.4 times more milk than 453 certified dairies in the state of Wisconsin (they are not all small, one Wisconsin dairy milk 600 cows).