The company cited the decline in consumption of cow's milk products;[15][16][17][18] rendering them unable to meet their debt and pension obligations.

In December, Dean Foods bought the Wells Dairy milk plant in Le Mars, Iowa.

[38][39] On May 12, 2008, the Cornucopia Institute filed a second complaint with the USDA again alleging that Deans Foods had violated federal organic regulations requiring access to pasture and fresh grass for their dairy cows.

[40] Silk brand soy milk was made using organic soybeans until early 2009, when Dean Foods switched to conventional soybeans while maintaining the same UPC barcodes and prices on the Silk products and replacing the word “organic” with “natural” on the product's packaging,[41] prompting the Cornucopia Institute to file complaints that the company had not properly notified retailers or consumers.

[42][43] Foremost Farms USA, a cooperative of over 2,000 dairy farmers in several mid-western states, sold its Wisconsin milk processing plants to Dean Foods in 2009.

[44] In January 2010, the US Department of Justice and the state attorneys general's office of Wisconsin and Michigan, filed a lawsuit objecting to the purchase and alleged that it created a monopolizing provider.

[46] In 2011, a class action suit was brought against Dean Foods over health claims made on the packaging of Horizon Organic Milk.

[48][49] In 2017, bettor and stock trader Billy Walters was convicted of insider trading in Dean shares in Federal court.