As a part of the Dos de Mayo (2 May) uprising the city had already successfully resisted a first siege from 15 June 1808 to 14 August 1808.

In order to achieve this, Napoleon wanted the exposed Spanish armies to remain in their current advanced positions.

On 21 November 1808, the French 3rd Corps crossed the Ebro River at Logrono and headed east towards Calahorra.

Palafox's deputy in the area, general O'Neylle demurred stating that he had strict orders not to cross the borders of Aragon (Tudela is located in Navarre).

To the west, a solid rampart had been built outside the city walls, incorporating the Augustinian and Trinitarian convents.

San Lazaro was fortified with a rampart protected by waterways and the two convents on the north side of the Ebro River had been made into fortresses.

On the key position of Monte Torrero, Sangenís built an entrenched military camp using the Aragon Canal as a moat.

Inside the walls, the strong, almost entirely inflammable masonry homes and apartment buildings were laced together with internal passageways, making each block of the city its own barricaded fortress, with the numerous church buildings standing as keeps and strong-points, from which grapeshot and counter-battery fire could command the streets.

These troops arrived from Germany on 15 December giving a total of 38,000 infantry, 3,500 cavalry, 3,000 engineers, and 60 siege guns to attack Saragossa.

Moncey then decided to concentrate his efforts on the southern side of the city and prepared attacks against the Pillar redoubt and against the San Jose convent.

The French preparations were finally complete on 10 January 1809 and they commenced bombarding the Pillar Redoubt and San Jose.

Palafox counter-attacked the French guns at 1 am on 11 January 1808 but this attack failed and the Spanish troops withdrew into the city.

The French attack on the Pillar Redoubt continued until the night of 15–16 January 1808 when the 1st Polish Vistula Regiment stormed the position.

Palafox knew the walls would not last long and prepared barricades in the city, turning it into a maze of small forts.

Lannes was concerned about his rear and recalled Mortier's division which had been protecting the lines of communication between Madrid and Saragossa.

Lannes broke through two breaches and captured the battery at the south-eastern corner and also the convent of Santa Engracia in the south-west.

Lannes, however, had decided on a slow block-by-block siege of each individual fortification in order to minimise French casualties.

However, French superiority in equipment and training took its toll, and thousands were falling daily both in the fighting and to disease, which was rampant throughout the city.

The French were unaware of this however and morale was low due to the apparent never-ending battle in the narrow streets.

The terms of surrender allowed private property to be respected and a general amnesty was granted to the city.

The city considered the Florence of Spain was completely destroyed, losing many emblematic buildings like Abbey of Santa Engracia or the houses of the kingdom, the government headquarters of the medieval era.