[4] Now known as Quinn's Chapel AME, its congregation is believed to have supported the Underground Railroad and aided fugitive slaves to freedom, together with members of the Antioch Baptist Church established in 1838.

An early interracial community, it suffered from structural discrimination; transport lines were routed to bypass and isolate it rather than connecting it, and economic development projects passed over it, and indeed were set up in competition to it.

'[6] According to oral history tradition, by 1829 "Mother" Priscilla Baltimore led a group of eleven families, composed of both fugitive and free African Americans, to flee slavery in St. Louis, Missouri.

They crossed the Mississippi River to the free state of Illinois, where they established a freedom village in the American Bottoms.

At one point, Quinn was captured by Missouri slave-catchers while on a missionary tour, but presented himself as a citizen of British India and was set free.

[13] In the late 19th century, its residents joined in taking new industrial jobs, commuting to those in East St. Louis and nearby areas.

"Blacks who migrated to what became known as Brooklyn were attracted to the possibilities of working in an industrialized settlement that would enjoy race autonomy and self-determinism.

Regional capital investment largely bypassed Brooklyn, taking place in the competing East St. Louis, Illinois, which gained the all-important railroad connection.

Tensions ran high with class and color conflicts by the early decades of the twentieth century, and evidence of political corruption.

In addition, with the growth in number of young, single male workers, attracted to industrial jobs, the demographics changed and family life in the village declined.

[15] In 1915, two rival gangs attempting to declare themselves police chief had a shootout in front of a grocery store, resulting in three deaths.

[18] With the decline of industry, from the mid-20th century on and the loss of jobs, Brooklyn has suffered high unemployment and problems similar to those of East St. Louis.

It lies along the southern margin of the Horseshoe Lake meander just north of the East St. Louis Mound Group of earthworks.

A team of archaeologists led by Dr. Joseph Galloy found evidence of early Afro-American occupation from 1830 to 1850, as well as material in other areas from 1850 to 1870.

This discovery suggests that the remains of Mother Baltimore's Freedom Village survive beneath the surface in Upper Brooklyn.

[21] Since the turn of the 21st century, residents have rallied around new work related to documentation of the village's rich historical past.

ISAS also helped the historical society to review documents to locate "Mother" Priscilla Baltimore's unmarked grave at Bellefontaine Cemetery in St. Louis.

[22] In addition, ISAS will assist the village in surveying the Brooklyn cemetery to detect gravesites and try to document the history.

[21] Surveys in 2008 revealed that "the archaeological record of Brooklyn lies intact beneath the extensive open spaces of current-day residential parcels.

In 2023, Landmarks Illinois added Brooklyn to 2023's list of Most Endangered Historic Places in Illinois, listing among its threats Brooklyn's decline in population and economy, high unemployment and low tax base, its lack of recognition for its history, and its sale of parcels to railroads that separate the community from the riverbank.

[citation needed] The town has a police department that in 2015 was described by the county prosecutor as having “gone from dysfunctional to nonfunctional.”[27] As of the census[32] of 2000, there were 676 people, 267 households, and 166 families residing in the village.