Despite the settings being France and continental Europe, it was filmed almost entirely in the UK and a bit in Malta. 

Filming Locations:

Dining Hall

In the Movie

Scene where Napoleon communicates with Josephine

In Reality

The scene was filmed in the Great Marble Hall of Blenheim Palace

Notre-Dame de Paris Cathedral

In the Movie

Scene where Napoleon crowns himself Emperor of France.

In Reality

The scene was filmed actually not in Paris, but in the main hall of Lincoln Cathedral in the city of Lincoln, UK.

Somerset House (as Place de la Révolution, Paris)

In the Movie

Scene where young Napoleon Bonaparte witnesses the execution of Marie Antoinette during the French Revolution in 1793. The courtyard is styled as Place de la Révolution, now Place de la Concorde in Paris: the guillotine stands here, and a dense crowd of revolutionaries gathers around, watching the grim spectacle.

In Reality

The scene was filmed in the central courtyard of Somerset House, a majestic neoclassical building on the Strand by the Thames in London. Built in the 18th century, it has served various state and cultural purposes, and today hosts exhibitions, events, and the famous winter ice rink. Its architecture convincingly portrayed revolutionary Paris.

St. Paul's Cathedral Square, Mdina (as the church scene of Toulon)

In the Movie

Scene where the moment arrives when Napoleon and Josephine stand together under the gates of St. Paul's Cathedral facing the square, and then after the liberation of prisoners following the siege, a separate church scene unfolds. The medieval Maltese architecture convincingly replaces the old French city streets needed for the plot.

In Reality

The scene was filmed on the main square in front of St. Paul's Cathedral in the fortified medieval city of Mdina in central Malta. Mdina, known as the Silent City, features narrow winding streets, medieval and Baroque architecture, and ancient stone buildings. The square in front of the cathedral provides a very accurate historical backdrop.

Fort Ricasoli, Malta (as the citadel during the Siege of Toulon)

In the Movie

Scene where it shows the French camp and the Siege of Toulon in 1793, where Napoleon first asserts his military talent. The fort, augmented with CGI, serves as the citadel housing British troops, and the scene conveys the fierce battle that began his rise as an emerging military star.

In Reality

The scene was filmed at the historic 17th-century fortress on the eastern side of the Grand Harbour in Kalkara, Malta. It was built by the Knights of the Order of St. John to defend the harbor entrance; its powerful bastions and extensive fortifications have made it sought after in film, especially for period war scenes.