The organization helps launch or improve TNR programs and expand affordable spay and neuter services.

[6] Deluged by requests for help with similar work, and aware of the lack of resources and information on the method, a network was formed for feral cats.

[6] In 2000, Alley Cat Allies halted a catch-and-kill order at Norfolk Naval Shipyard in Portsmouth, Virginia, and instead instituted a TNR program, becoming the first animal protection group in the nation to hold a formal contract with the U.S.

[12] In 2018, Marc Gunther of The Chronicle of Philanthropy wrote that fiscal and organizational practices at Alley Cat Allies demonstrated a broader issue wherein "the vast majority of charities get little or no critical examination from ratings groups or regulators".

[13] Gunther reported that Alley Cat Allies had bought two homes, for $590,000 and $569,000, without disclosure to its full board.

[13] In November 2021, Alley Cat Allies filed a petition in the Supreme Court of Appeals of West Virginia for a writ of mandamus against Berkeley County Animal Control, based in Berkeley County, West Virginia.

[22] Alley Cat Allies filed a lawsuit in March 2024 against the U.S. National Park Service four months after the federal agency announced it would contract an animal welfare organization to remove an estimated 200 cats that live in an area surrounding a historic seaside fortress in Old San Juan, Puerto Rico.