The company, based in the docks area, posted revenues of £4.13m, up from £3.78m, while pre-tax profits fell to £42,237 from £167,749 in the year to 31 March 2012.
The fall came as the company benefits from a new partnership with the Elvis Presley Graceland attraction in Memphis.
The Beatles Story was established in 1988, opening in the newly developed Albert Dock in May 1990.
Merseytravel bought the tourist attraction in 2008 and the public transport body now runs the Beatles Story alongside other attractions including the ferries, Spaceport, the U-Boat Story and the Mersey Tunnel Tours.
In 2008, the attraction tripled in size from 8,000 sq ft to 23,000 sq ft to add new areas, an expanded store and a Starbucks.
The following year it expanded into a second site, with the Beatles Story Pier Head housed at the new Merseyferries terminal.
Earlier this year, the city started to welcome overnight stays from turnaround cruises rather than those just staying for the day.
Notes accompanying the newly filed accounts said: "The launch of the major partnership between Graceland and The Beatles Story, which commenced in October 2011 at the Pier Head, continues to attract visitors who are interested in the link between the two "greats".
"Directors and management strive to extend The Beatles Story into new areas to attract further visitors.
"The increased cruise ships that are stopping at Liverpool will hopefully increase visitors into the attractions.
"Whilst trading conditions remain fragile, and could be susceptible to any deterioration in the global economy, the directors believe that appropriate steps have been put in place to ensure that the financial performance of The Beatles Story remains strong."