The original town plat was a simple nine-block grid on the east side of the Wapsipinicon River.

The town was intended as an alternative to Quasqueton (then called Quasequetuk), which was the county seat prior to 1847.

On Main Street, on the west bank of the Wapsipinicon, a six-story grist mill was built in 1867.

Some structural restoration occurred in recent years, and the mill now functions partly as an historical museum.

A courthouse was built in 1857, on the east side of the town, on a site described at that time as "the highest tract of land in the neighborhood," where offers "a fine view of the city of Independence, the Valley of the Wapsipinicon, and the surrounding Country".

For a few years in the late 1880s and early 1890s, Independence was a nationally known horse-racing center, and was sometimes referred to as the "Lexington of the North".

A telegraph operator and creamery owner from nearby Jesup, Iowa, Williams (with no experience in breeding horses) purchased in 1885 two mares, each of which within a year gave birth to a stallion.

These two stallions, which Williams named Axtel and Allerton, went on the set world trotting records, with the result that Williams' earnings enabled him to publish a racing newspaper titled The American Trotter, to build a large three-story hotel and opera house called The Gedney, and to construct a figure-eight shaped race track on the west edge of town, on a large section of land called Rush Park, where he also built a magnificent horse barn, his family mansion, and peripheral structures.

Today, the location of Williams' race track (which was the original site of the Buchanan County Fairgrounds) is a corn field.

His house is still standing, but, in recent years, the Rush Park barn was demolished by a bulldozer, to make way for a fastfood drive-in and an auto parts store.

In the years that followed the race track days, the town lost most of its importance when the railroad terminal at Independence was pushed further west to Waterloo, Iowa.

While living in Paris, Stein became close friends with an American expatriate painter named William Edwards Cook, who was born in Independence in 1881.

It was Cook who taught Stein how to drive (so that she could transport supplies for the French during World War I).

In 1933, when Stein traveled throughout the U.S. on a book publicity tour, she eagerly agreed to speak at Iowa City (on the second floor of what is now the Prairie Lights Bookstore), with the provision that she would be able to fly over Independence, to see Cook's birthplace from the air.

Unfortunately, the Midwest was hit by a major winter storm that day, and Stein's visit to Iowa was entirely cancelled.

The race track at Rush Park has also the distinction of being the site of the first one-mile bicycle speed record of under two minutes, which was set in 1892 at Independence by John S. Johnson.

In 2011, the communities of Brandon, Rowley and Independence passed a bond referendum to build a new $27,500,000 junior and senior high school that opened in the fall of 2013.