Windaroo was the second sugar lease taken out in the Albert River Region by J. S. Pinwell. It was later run by William Warren who also had Noyea Plantation, now known as Mount Warren Park. The Heck family, who own the Rocky Point sugar mill, took up the estate in the 1894 and continued to grow sugar along the flats, while grazing cattle on the slopes.

The area remained essentially rural until the late 1970s when a rural residential estate, Windaroo Acres, was subdivided. Land was first released for sale in 1983 in lots ranging from 4,054 to 8,071 square metres. Although located near to Mount Warren Park, Windaroo also has a golf course and a range of sporting facilities. The Windaroo Golf Club opened in 1981.

Windaroo Cottage was renovated by Jim and Ann Hart after they purchased it in 1974. It had been relocated to the site from the Beenleigh Rum Distillery some years earlier and had been home to a widow with seven children. The Harts established a gallery in the cottage and in 2003 it was again renovated by new owner Wendy Child. At that time it was a function venue.

In 1989 the Country Club opened an a la carte restaurant. In 1990 the Heck family offered part of the estate which included the golf course for sale. It was purchased by developer Chris Kerwick of Chima Pty Ltd. Further upgrade to the golf club and its facilities were undertaken in time for the 1993 Queensland Open Golf Championship. In 1995, Villa World purchased the last vacant land on the estate to develop a range of house and land packages. The Windaroo Shopping Village opened in April 1996.

Windaroo State School opened in January 1992. In 1993 approval was given for the construction of a State High School to be known as Bahr's Scrub State High, as that was the official suburb name at the time. When it opened in 1994 it became known as Windaroo Valley High School. The school continued to expand and in 1996 a performing arts centre was opened. Plans were then put in place to develop a visual arts building, music building and a gymnasium.

In 2002 the country club was sold to Albert Valley Properties to develop a gated community, which included townhouses.