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While in the Bahamas, Bonny began mingling with pirates in the local taverns. She met John "Calico Jack" Rackham, captain of the pirate sloop Revenge, and Rackham became her lover. Rackham offered Bonny's husband James Bonny money in exchange for her, but her husband refused. Anne and Rackham escaped the island together and Bonny became a member of Rackham's crew. She disguised herself as a man on the ship and only Rackham and eventually Mary Read knew about her true gender. They had a son in Cuba. Many different theories state that he was left with his family or simply abandoned. Bonny rejoined Rackham and continued the pirate life, having divorced her husband and marrying Rackham while at sea. Bonny, Rackham, and Mary Read stole the ship William, then at anchor in Nassau harbour, and put out to sea.[12] Rackham and the two women recruited a new crew. Their crew spent years in Jamaica and the surrounding area.[13] Over the next several months, they enjoyed success, capturing many, albeit smaller, vessels and bringing in abundant treasure.

Some scholars suggest Bonny was in a romantic relationship with Read.

Bonny took part in combat alongside the men, and the accounts of her exploits present her as competent, effective in combat, and respected by her shipmates. Governor Rogers had named her in a "Wanted Pirates" circular published in the continent's only newspaper, The Boston News-Letter.[11] Although Bonny was historically renowned as a Caribbean pirate, she never commanded a ship of her own.