By 1799 seven years' continuous fighting had begun to tell on a physique even as strong as Lefèbvre's, and the general applied for lighter work as commander of the Directory Guard, and later, for sick leave; but the commencement of the campaign against the Archduke Charles, in the valley of the Danube, once again stimulated his indefatigable appetite for active service. Though suffering from scurvy and general overstrain, he took his share in the hard fighting at Feldkirche and Ostrach, but a severe wound received in the latter combat at last compelled him to leave the field and go into hospital.

On his return to France he was entrusted by the Directory with the command of the 17th military district, with Paris as its headquarters. The task was a difficult one, as the numerous coups d'état had shaken both public morality and military discipline. Among other unpleasantnesses the commander of Paris found himself on one occasion forced to place a general officer in the Abbaye, the civil prison, for flatly refusing to obey orders. But, difficult as his task was, the situation became much more complicated by the sudden return of Bonaparte from Egypt. Bonaparte arrived in Paris with the fixed determination to assume the reins of government. It was clear to so staunch a republican as Lefèbvre that all was not well with the Republic under the Directory, and it seemed as if Bonaparte, shimmering in the glamour of Italy and Egypt, was the sole person capable of conciliating all parties and of bringing the state of chronic revolution to an end. Directly he met the famous Corsican the simple soldier fell an easy victim to his personality; while Bonaparte was quick to perceive what a great political asset it would be if Lefèbvre, the republican of the republicans, the embodiment of the republican virtues, could be bound a satellite in his train. On the morning of the 18th Brumaire, the commander of the Paris Division was the first to arrive of all the generals whom the plotter had summoned to his house; he was puzzled to find that troops were moving without his orders, and he entered in considerable anger. Bonaparte at once explained the situation. The country was in danger, foes were knocking at the door, and meanwhile the Republic lay the prey of a pack of lawyers who were exploiting it for their own benefit without thought of patriotism. "Now then, Lefèbvre," said he, "you, one of the pillars of the Republic, are you going to let it perish in the hands of these lawyers? Join me in helping to save our beloved Republic. Look, here is the sword I carried in my hand at the battle of the Pyramids. I give it to you as a token of my esteem and of my confidence." Lefèbvre could not resist this appeal; his warm and generous nature responded to the artful touch; grasping the treasured sword with tears in his eyes, he swore he was ready "to throw the lawyers in the river." With a sigh of relief Bonaparte put his arm through Lefèbvre's and led him into his study, and for the next fourteen years he remained, as he thought, the confidential right-hand man of the great-hearted patriot, but in reality the tool, dupe, and stalking-horse of a wily adventurer.

The general accompanied Napoleon to the Tuileries and listened to the carefully chosen words: "Citizens Representatives, the Republic is perishing; you know it well, and your decree can save it. A thousand misfortunes on all who desire trouble and disorder. I will oust them, aided by all the friends of liberty.... I will support liberty, aided by General Lefèbvre and General Berthier, and my comrades in arms who share my feelings.... We wish a Republic founded on liberty, on equality, on the sound principles of national representation. We swear this: I swear this; I swear in my own name and in the name of my comrades in arms." Later in the day, during the struggle at the Orangerie, it was Lefèbvre who saved Lucien Bonaparte and cleared the hall with the aid of some grenadiers.

From the 18th Brumaire Napoleon, as First Consul, and later as Emperor, held in Lefèbvre a trump card whereby he could defeat any attempted hostile combination of the republicans. Hence it was that, at the time of the proclamation of the Empire, he included him in his list of Marshals, to prove as it were that the Empire was merely another form of the Republic. Later still, for the same reason, when he was making his hierarchy stronger, he created him one of his new Dukes.

The immediate reward for Lefèbvre's support during the coup d'état was a mission to the west to extinguish the civil war in La Vendée. The general was lucky in surprising a considerable force of rebels at Alençon, and soon fulfilled his work, and received the further reward of a seat as Senator, which brought in an income of 35,000 francs a year. When the list of Marshals was published he was bracketed with Kellermann, Pérignon, and Serurier as "Marshals whose sphere of duty would lie in the Senate." As such, at the coronation of the Emperor in Notre Dame he held the sword of Charlemagne, while Kellermann carried the crown. Strong in his trust of him, Napoleon had, in 1803, created him Prætor of the Senate. But fortune did not destine that he should long enjoy his honours in peace. Thanks to his magnificent physique a few years of rest entirely restored his health. The wound, which in 1799 had threatened to incapacitate him permanently, had completely healed, and in 1806 he once again found himself on active service. The Emperor knew well that the Marshal was a sergeant-major rather than a strategist, and accordingly placed him at the head of the Guard, where his powers of discipline could be utilised to the full without calling on him to solve any difficult problems. At Jena the Guard had plenty of hard fighting such as their commander loved. A few days later the Marshal proved that the Guard could march as well as fight, when, at nine o'clock on the evening of October 24th, the regiments marched into Potsdam after covering forty-two miles since the morning.

Early in 1807 the Emperor entrusted the Marshal with the siege of Dantzig, a strong fortress near the mouth of the Vistula, well-garrisoned by a Prussian force of fourteen thousand under Marshal Kalkreuth. Lefèbvre, conscious of his lack of engineering skill, was afraid of undertaking the task, but the Emperor promised to send him everything necessary, and to guide him himself to the camp of Finkenstein, and ultimately said goodbye to him with the words, "Take courage, you also must have something to speak about in the Senate when we return to France." The siege lasted fifty-one days, during which the Marshal took scarcely a moment's rest: ever in the trenches, heading every possible charge, calling out to the soldiers, "Come on, children, it's our turn to-day," or "Come on, comrades, I am also going to have a turn at fighting." Such treatment worked wonders with the fiery French, but the sluggish men of Baden, who formed a considerable part of his force, were not accustomed to be so hustled, and the Marshal's camp manners grated on the Prince of Baden, who considered "that the Marshal's staff was mostly composed of men of little culture, and that his son held the first place among those who had no manners." The Emperor had to write to his fiery lieutenant, "You treat our allies without any tact; they are not accustomed to fire, but that will come. Do you think that our men are as good now as in 1792—that we can be as keen to-day after fifteen years' war? Pay what compliments you can to the Prince of Baden ... you cannot throw down walls with the chests of your grenadiers ... let your engineers do their work and be patient.... Your glory is to take Dantzig; when you have done that you will be content with me." It was hard for the Marshal to show patience, for he knew but one way to do a thing, and that was to go straight at it as hard as he could. As one of the privates said, "The Marshal is a brave man, only he takes us for horses." With Lannes and Mortier sent to reinforce him, it was still more difficult to show patience. But the end came, and on the fifty-first day of the siege Marshal Kalkreuth surrendered, and the two other Marshals had the generosity to allow Lefèbvre to enjoy alone all the honours of the conquest.

In the next year the Emperor had determined to strengthen his throne by the creation of a new nobility. It was important to see how Republican France would greet this scheme, and accordingly Napoleon determined to include Lefèbvre among his new Dukes. One day the Emperor sent an orderly officer with orders to say to the Marshal, "Monsieur le Duc, the Emperor wishes you to breakfast with him, and asks you to come in a quarter of an hour." The Marshal did not hear the title and merely said he would attend. When he entered the breakfast-room the Emperor went up to him, shook hands with him, and said, "Good-morning, Monsieur le Duc; sit by me." The Marshal, hearing the title, thought he was joking. The Emperor, to further mystify him, said, "Do you like chocolate, Monsieur le Duc?" "Yes, sire," replied the Marshal, still mystified. Thereon the Emperor went to a drawer and took out a packet labelled chocolate; but when the Marshal opened the box he found it contained one hundred thousand écus in bank notes. While in the army the new Duke was warmly congratulated on his honours, at Paris the smart ladies and Talleyrand did their best to annoy the Duchess. Numerous were the cruel tales they spread of her lack of breeding and of her Amazon ways; how, when the horses bolted with her carriage, she seized the coachman by the scruff of his neck and by main force pulled him off the seat and herself stopped the runaways. But, quite unmoved, the Duchess pursued her course, visiting the sick, giving away large sums to charities, lending a helping hand to any friend in difficulties, and as usual prefacing her remarks by "When I used to do the washing."

When, in the autumn of 1808, Napoleon realised how serious was the Spanish rising, he despatched his Guard to the Peninsula under the Duke of Dantzig. But the war brought few honours to any one, and the Marshal proved once again that he could neither act independently nor assist in combinations with patience. He nearly spoiled Napoleon's whole plan of campaign by a premature move against Blake, prior to the battle of Espinosa. From Spain the Guard was hurriedly recalled on the outbreak of the Austrian campaign of 1809. The Marshal, in command of the Bavarian allies, did yeoman service under Napoleon's eye during the great Five Days' Fighting. He was present also at Wagram, and immediately after that battle was despatched to put down the rising in the Tyrol. During the Russian campaign he once again commanded the Guard, taking part in all the hard fighting of the advance and also in the horrors of the retreat. Though in his fifty-eighth year the tough old soldier marched on foot every mile of the way from Moscow to the Vistula, and shared the privations of his men, watching over his beloved Emperor, his little "tondu de caporal," with the care of a woman, himself mounting guard over him at night and surrounding him with picked men of the Guard. To add to the trials of that dreadful campaign the Duke lost at Vilna his eldest son, a most promising young soldier who had already reached the rank of general. This blow and the strain of the retreat were too much for him, and he was unable to assist the Emperor in the campaign of 1813. But when the Allies invaded the sacred soil of France the old warrior put on harness again and fought at Montmirail, Arcis-sur-Aube and Champaubert, where he had his horse killed under him. At Montereau he fought with such fury that "the foam came out from his mouth."

While the Marshal was spending his life-blood in the field, the Duchess in Paris was fighting the intrigues of the royalist ladies. When an insinuation was made that the Duke might be won over from the Emperor, the Duchess despatched a friend to the army commanding him "to return to the army and tell my husband that if he were capable of such infamy I should take him by the hair of his head and drag him to the Emperor's feet. Meanwhile, inform him of the intrigues going on here." On April 4th the end came. The Marshals refused to fight any longer, and, after Napoleon's abdication, Lefèbvre, with the others, went to Paris to treat with Alexander. The Emperor was gone, but France remained, and it was thanks to Kellermann and Lefèbvre that Alsace was not wrested from her, for they so strongly impressed Alexander by their arguments that he decided to oppose the Prussians, who desired to strip France of her eastern provinces.

The Marshal swore allegiance to the Bourbons and duly received the Cross of St. Louis and his nomination as peer of France. With the year's peace came time for reflection, and he began to see that "son petit bonhomme de Sire," as he called Napoleon, had merely used him as a political pawn in his endeavour to bind the republicans to the wheel of the imperial chariot. Accordingly, when the Emperor returned from Elba he was not among those who rushed to meet him. Still, although he had no personal interview with the Emperor during the Hundred Days, he so far compromised himself as to accept a seat in the Senate. For this conduct he was under a cloud for the first years of the second Restoration, but in 1819 he was pardoned and restored to his rank and office.