On 29 May 1802, now a chef de brigade (colonel), Habert received command of the 105th Line Infantry Regiment.
He became a chevalier of the Légion d'Honneur in 1803 and an officer of the Légion in 1804.
During this time his unit guarded the west coast of France.
In August 1805, at the start of the War of the Third Coalition, his regiment joined Jacques Desjardin's division of Marshal Pierre Augereau's VII Corps.
Having a long march from the environs of Brest, Augereau's men missed the bulk of the fighting but managed to trap Franz Jellacic's Austrian division near Lake Constance.
On 13 November, Augereau with Desjardin's 1st Division forced Jellacic to surrender his 4,000 troops in the Capitulation of Dornbirn in the Vorarlberg.
The Austrians were allowed to march off to Bohemia on condition that they would not fight against France for one year.

The beginning of the War of the Fourth Coalition saw Habert's 105th Regiment serving in Jacques Lefranc's brigade of Desjardin's VII Corps Division.
At the Battle of Jena on 14 October 1806, Desjardin's division seized the village of Isserstadt, piercing the right-center of the Prussian-Saxon front and rescuing Marshal Michel Ney's advance guard from a precarious situation.

 
On 24 December, Augereau forced a crossing of the Wkra River in Poland in the Battle of Czarnowo.
He sent Étienne Heudelet de Bierre's 2nd Division to attempt a passage at Sochocin, while Desjardin tried to cross at Kołoząb.
A Russian division under Michael Andreas Barclay de Tolly opposed the French.
Heudelet's attack was repulsed, but Desjardin met with success.
Desjardin pinned down the Russians with covering fire, while some elite companies stormed across the partially destroyed bridge.
Pierre Belon Lapisse led Desjardin's other brigade in a flank attack.
The combined assault drove off the Russian defenders and captured six field pieces.

Habert led the 105th against the Russians at the Battle of Golymin on 26 December.
Desjardin's division reached the field first and pressed back a Russian infantry regiment.
Reinforced, the Russians pushed back Desjardin's men, who rallied and came on again.
This time Desjardin's 2nd Brigade was stopped by grapeshot only 50 paces from the enemy guns.
The brigade fell back 200 yards and formed squares in front of the village of Kaleczin.
The Russians retreated that night.

The 105th fought at the Battle of Eylau on 8 February 1807.
At 2:00 PM in the afternoon, Emperor Napoleon ordered an unwell Augereau to attack the Russian left flank.
As the movement got underway, a blizzard swept across the battlefield.
Blinded by the snow, the VII Corps veered to the left of its intended attack axis to strike the Russian center.
Pounded unmercifully by a 70-gun battery and swamped by counterattacking infantry and cavalry, Augereau's soldiers suffered huge losses and the remnants fled.
His division commander Desjardin was killed.
The decimated VII Corps was discontinued and the survivors distributed to other corps.
Habert was transferred to Claude Legrand's division in Marshal Nicolas Soult's IV Corps on 21 February.
He fought at the Battle of Heilsberg on 10 June 1807 where he was wounded in the head and shoulder.
On 11 July 1807 he became a commandant in the Légion d'Honneur.
On 29 May 1802, now a chef de brigade (colonel), Habert received command of the 105th Line Infantry Regiment. He became a chevalier of the Légion d'Honneur in 1803 and an officer of the Légion in 1804. During this time his unit guarded the west coast of France. In August 1805, at the start of the War of the Third Coalition, his regiment joined Jacques Desjardin's division of Marshal Pierre Augereau's VII Corps. Having a long march from the environs of Brest, Augereau's men missed the bulk of the fighting but managed to trap Franz Jellacic's Austrian division near Lake Constance. On 13 November, Augereau with Desjardin's 1st Division forced Jellacic to surrender his 4,000 troops in the Capitulation of Dornbirn in the Vorarlberg. The Austrians were allowed to march off to Bohemia on condition that they would not fight against France for one year.
The beginning of the War of the Fourth Coalition saw Habert's 105th Regiment serving in Jacques Lefranc's brigade of Desjardin's VII Corps Division. At the Battle of Jena on 14 October 1806, Desjardin's division seized the village of Isserstadt, piercing the right-center of the Prussian-Saxon front and rescuing Marshal Michel Ney's advance guard from a precarious situation.
 
On 24 December, Augereau forced a crossing of the Wkra River in Poland in the Battle of Czarnowo. He sent Étienne Heudelet de Bierre's 2nd Division to attempt a passage at Sochocin, while Desjardin tried to cross at Kołoząb. A Russian division under Michael Andreas Barclay de Tolly opposed the French. Heudelet's attack was repulsed, but Desjardin met with success. Desjardin pinned down the Russians with covering fire, while some elite companies stormed across the partially destroyed bridge. Pierre Belon Lapisse led Desjardin's other brigade in a flank attack. The combined assault drove off the Russian defenders and captured six field pieces.
Habert led the 105th against the Russians at the Battle of Golymin on 26 December. Desjardin's division reached the field first and pressed back a Russian infantry regiment. Reinforced, the Russians pushed back Desjardin's men, who rallied and came on again. This time Desjardin's 2nd Brigade was stopped by grapeshot only 50 paces from the enemy guns. The brigade fell back 200 yards and formed squares in front of the village of Kaleczin. The Russians retreated that night.
The 105th fought at the Battle of Eylau on 8 February 1807. At 2:00 PM in the afternoon, Emperor Napoleon ordered an unwell Augereau to attack the Russian left flank. As the movement got underway, a blizzard swept across the battlefield. Blinded by the snow, the VII Corps veered to the left of its intended attack axis to strike the Russian center. Pounded unmercifully by a 70-gun battery and swamped by counterattacking infantry and cavalry, Augereau's soldiers suffered huge losses and the remnants fled. His division commander Desjardin was killed. The decimated VII Corps was discontinued and the survivors distributed to other corps. Habert was transferred to Claude Legrand's division in Marshal Nicolas Soult's IV Corps on 21 February. He fought at the Battle of Heilsberg on 10 June 1807 where he was wounded in the head and shoulder. On 11 July 1807 he became a commandant in the Légion d'Honneur.
Pierre-Joseph Habert