After the treaty of Pressburg, on December 27, 1805, Napoleon quitted the army and returned to Paris, leaving the major-general in command of the Grand Army with orders to evacuate the conquered territory when the terms of the treaty had been carried out by the Austrians; but the Emperor retained the real control, and every day a courier had to be despatched to Paris with a detailed account of every event, and every day a courier arrived from Paris bearing fresh orders and instructions. For Napoleon refused to allow the slightest deviation from his orders: "Keep strictly to the orders I give you," he wrote; "execute punctually your instructions. I alone know what I want done." Meanwhile the major-general was still War Minister and had to supervise all the more important business of the War Office; while he also found time to edit an official history of the campaign of 1805, and to superintend the execution of a map of most of the Austrian possessions. The work was immense, but Berthier never flagged, and the Emperor showed his appreciation of his zeal when on March 30th, 1806, he conferred on him the principality of Neuchâtel with the title of Prince and Duke, to hold in full possession and suzerainty for himself, his heirs and successors, with one stipulation, that he should marry. He added that the Prince's passion for Madame Visconti had lasted too long, that it was not becoming to a dignitary of the Empire, and that he was now fifty years old and ought to think of providing an heir to his honours. The Prince Marshal never had time to visit personally his principality, but he sent one of his intimate friends, General Dutaillis, to provide for the welfare of his new subjects, and to the best of his ability he saw that they were well governed, while a battalion of picked troops from Neuchâtel was added to the Imperial Guard. But, orders or no orders, the Prince could never break himself free from the trammels of his mistress, and Napoleon gave him but little leisure in which to find a congenial partner, so that it was not till after Tilsit, in the brief pause before the Peninsular War, that Berthier at last took a wife. His chosen Princess was Elizabeth, the daughter of William, Duke of Bavaria, brother of the King. She was married with all due solemnity in March, 1808, and though the exigencies of war gave her but little opportunity of seeing much of her husband, affection existed between them, as also between Berthier and his father-in-law, the Duke of Bavaria. All cause of difficulty was smoothed over by the fact that in time the Princess herself conceived an affection for Madame Visconti.

By September, 1806, the Grand Army had evacuated Austria, and the Prince Marshal was hoping to return to Paris when suddenly he was informed by the Emperor of the probability of a campaign against Prussia. On the 23rd definite orders arrived indicating the points of assembly; by the next day detailed letters of instructions for every corps had been worked out and despatched by the headquarters staff. Napoleon himself arrived at Würzburg on October 2nd, and found his army concentrated, but deficient of supplies. At first his anger burst out against the chief of the staff, but a moment's reflection proved to him that there was not sufficient transport in Germany to mass both men and supplies in the time he had given, and he entirely exonerated Berthier, who by hard work contrived in three days to collect sufficient supplies to allow of the opening of the thirty days' campaign which commenced with Jena and ended by carrying the French troops across the Vistula. The fresh campaign in the spring of 1807 was attended by an additional difficulty, there existed no maps of the district, and the topographical department of the staff was worked off its legs in supplying this deficiency. Meanwhile, during the halt after Pultusk, the major-general was busy re-clothing and re-equipping the army and hurrying up reinforcements; while in addition to the work of the War Office he had to supervise the French forces in Italy and Naples. After Tilsit, as after Pressburg, Napoleon hurried back to France and left the Prince of Neuchâtel to arrange for the withdrawal of the Grand Army, and it was not till July 27th that Berthier at last returned to Paris.

The Prince came back more than ever dazzled by the genius of the Emperor; not even Eylau had taught him that there were limits to his idol's powers. But with more than eight hundred thousand men on a war footing, with divisions and army corps scattered from the Atlantic to the Niemen, from Lübeck to Brindisi, it was impossible for one man to be at once chief of the staff and Minister of War. Accordingly, on August 9th the Emperor made General Clarke Minister of War, and, to show that this was no slight on his old friend, on the same day he created the Prince of Neuchâtel Vice-constable of France. For the next three months Berthier was able to enjoy his honours at his home at Grosbois, or in his honorary capacity at Fontainebleau, but in November the Emperor carried him off with him to Italy on a tour of inspection. During the whole of this holiday in Italy the Prince was busy elaborating the details of the coming campaign in Spain, and it was the Spanish trouble which cut short his honeymoon, for on April 2nd he had to start with the Emperor for Bayonne. From the outset the Prince warned the Emperor that the question of supplies lay at the root of all difficulties in Spain; but Napoleon clung to his idea that war should support war, and Berthier knew that it was hopeless to attempt to remove a fixed idea from his head, and, still believing in his omnipotence, he thought all would be well. Meanwhile, as the summer went on, it was not only Spain that occupied the Prince's attention, for the conquest of Denmark had to be arranged, and the passes in Silesia and Bohemia carefully mapped, in view of hostilities with Prussia or Austria. Early in August Berthier was at Saint Cloud making arrangements to reinforce Davout in Silesia, owing to the growing hostility of Austria, when, on the 16th, arrived the news that Joseph had had to evacuate all the country west of the Ebro. But Napoleon and Berthier could not go to his help until after the imperial meeting at Erfurt in September. However, on reaching Spain, the magic of the Emperor's personality soon restored the vigour and prestige of the French arms. Still the Prince Marshal could not hide from himself that all was not as it used to be; Napoleon's temper was more uncertain, and the Marshals, smarting under reprimands, were not pulling together. When the Emperor returned to France, after having missed "the opportunity of giving the English a good lesson," he left Berthier behind for a fortnight "to be sure that King Joseph had a proper understanding of everything." But trouble was bound to come, for the Emperor himself was breaking his own canon of the importance of "the unity of command" by nominally leaving Joseph in control of all the troops in Spain, but at the same time making the Marshals responsible to himself through the major-general.

In 1809 Napoleon made another grave mistake. He had calculated that Austria could make no forward movement before April 15th, and accordingly he sent Berthier early in March to take temporary command of the Grand Army, with instructions to order Davout to concentrate at Ratisbon and Masséna at Augsburg. His idea was that there would be ample time later to order a concentration on either wing or on the centre. But the Austrians were ready quite a fortnight before he had calculated. The major-general kept him well informed of every movement of the enemy, and pointed out the dangerous isolation of Davout. Still the Emperor did not believe the Austrian preparations were so forward; and a despatch from Paris, written on April 10th, which arrived at headquarters at Donauwörth on the 11th, ordered the major-general to retain Davout at Ratisbon and move his own headquarters there, "and that in spite of anything that may happen." Unfortunately, a semaphore despatch sent a few hours later, when Napoleon had really grasped the situation, went astray and never reached Berthier. The Prince of Neuchâtel understood as clearly as any one the dangerous position of Davout; the Duke of Eckmühl himself thought that the major-general was trying to spoil his career by laying him open to certain defeat; depression spread through all the French corps. But after years of blind devotion to his great chief Berthier could not steel himself to break distinct orders, emphasised as they were by the expression "in spite of whatever may happen," and a great catastrophe was only just averted by the arrival of Napoleon, who at once ordered Davout to withdraw and Masséna to advance. Berthier himself was visited by the full fury of the Emperor's anger. But the cloud soon passed, for Berthier was as indispensable as ever, and more so when, after the failure at Aspern-Essling, immense efforts had to be made to hurry up troops from every available source. At the end of the campaign the Emperor justly rewarded his lieutenant by creating him Prince of Wagram.

Once again Napoleon left Berthier to arrange for the withdrawal of the army, and it was not till December 1st that the Prince of Wagram regained Paris and took up the threads of the Peninsular campaign. His stay there was short, for by the end of February he was back again in Vienna, this time not as major-general of a victorious army, but as Ambassador Extraordinary to claim the hand of the Archduchess Marie Louise for his master, the Emperor Napoleon, and to escort her to her new home. For the next two years the Prince remained at home at Grosbois or on duty at Fontainebleau, but in spite of great domestic happiness he was much worried by the terrible Spanish war. No one saw more clearly that every effort ought to be made to crush the English, but he was powerless to persuade the Emperor, and he had to endure to the full all the difficulties arising from breaking the "unity of command." No one understood better what hopeless difficulties would arise when Napoleon ordered him to write, "The King will command the army.... The Guard does not form part of the army." To add to these troubles, it became more and more evident that Germany was riddled with secret societies and that war with Russia was inevitable. So it was with a sigh of relief that in January, 1812, he received the order to turn his attention from Spain and resume his functions as major-general of the Grand Army. Not that he desired further active service; like many another of the Emperor's soldiers, he mistrusted the distant expedition to Russia, and feared for the honour and safety of France. Already in his sixtieth year, there was little he could gain personally from war. As he said to Napoleon, "What is the good of having given me an income of sixty thousand pounds a year in order to inflict on me the tortures of Tantalus? I shall die here with all this work. The simplest private is happier than I." The Emperor, knowing the attitude of many of his Marshals, and himself feeling the strain of this immense enterprise, was unusually irritable. Consequently relations at headquarters were often strained, and the Marshals were angry at the severe reprimands to which they were subjected. The controlling leaders being out of gear the machine did not run smoothly: there was nothing but friction and tension. The Marshals were inclined to attribute their disgrace to the ill-will of Berthier and not to the temper of Napoleon. Particularly was this the case with Davout, who since 1809 had suspected that Berthier desired to ruin his reputation. Accordingly the Prince of Eckmühl set down the succession of reprimands which were hurled at his head to the machinations of the major-general, and not, as was the case, to Napoleon's jealousy of him, because people had prophesied he would become King of Poland. This misunderstanding was most unfortunate, for it prevented Berthier from effecting a reconciliation between Davout and the Emperor. Hence Napoleon was driven more and more to trust to the advice of the rash, unstable King of Naples. The major-general's lot through the campaign was most miserable. Working day and night to supervise the organisation of the huge force of six hundred thousand men; mistrusted by his former comrades; blamed for every mishap by the Emperor, whatever the fault might be, he had to put up with the bitterest insults, and while working as no other man could work, to endure such taunts as, "Not only are you no good, but you are in the way." Everything that went wrong "was the fault of the general staff, which is so organised that it foresees nothing," whether it was the shortcomings of the contractors or the burning of their own magazines by the Russians. But what most moved Napoleon's anger against the chief of the staff was that Berthier, with "the parade states" before him, emphasising the enormous wastage of the army, constantly harped on the danger of pressing on to Moscow. So strained became the relations between them, that for the last part of the advance they no longer met at meals. But during the hours of the retreat the old friendship was resumed. Berthier bore no malice, and showed his bravery by himself opposing the enemy with musket and bayonet; and on one occasion, with Bessières, Murat, and Rapp, he saved the Emperor from a sotnia of Cossacks.

When Napoleon quitted the army at Vilna he left the major-general behind to help the King of Naples to withdraw the remnant of the Grand Army. Marching on foot through the deep snow, with fingers and nose frostbitten, the sturdy old veteran of sixty endured the fatigue as well as the hardiest young men in their prime; and in addition to the physical fatigue of marching, had to carry out all the administrative work, and bear the moral responsibility for what remained of the army; for the King of Naples, thinking of nothing but how to save his own crown, when difficulties increased, followed the example of Napoleon and deserted his post. Thereon the major-general took on himself to nominate Prince Eugène as Murat's successor. But in the end his health gave way, and the Emperor himself wrote to Prince Eugène telling him to send the old warrior home.

Berthier reached Paris on February 9th, much broken down in health; but his wonderful physique soon enabled him to regain his strength, and by the end of March he was once again hard at work helping the Emperor to extemporise an army. With his complete knowledge of this force, no one was more astonished than Berthier at the successes of Lützen and Bautzen, and no one more insistent in his advice to the Emperor to accept the terms of the Allies during the armistice; but he advised in vain. Then followed the terrible catastrophe of Leipzig, due undoubtedly to Berthier's dread of acting without the express orders of the Emperor. The engineer officer charged with preparing the line of retreat reported that the one bridge across the Elster was not sufficient. The major-general, knowing that the Emperor desired to hide any signs of retreat from the Allies, replied that he must await the Emperor's orders, so, when, after three days' fighting, the retreat could no longer be postponed, a catastrophe was inevitable.

Yet, in spite of everything, the Emperor refused to acknowledge himself beaten, and by the commencement of 1814 was once again ready to take the field, though by now the Allies had invaded France. Loyal as ever, Berthier worked his hardest; but he once again incurred the Emperor's anger by entreating him to accept the terms offered him at Châtillon. Still, when the end came and Napoleon abdicated, Berthier remained at his side, and it was only when the Emperor had released his Marshals from their allegiance that on April 11th he sent in his adhesion to the new government. When all save Macdonald had deserted the fallen Emperor, Berthier stayed on at Fontainebleau, directing the withdrawal of the remnants of the army, and making arrangements for the guard which was to accompany Napoleon to Elba. But though he remained with him until the day before he started for Elba, Berthier refused to share his exile, and at the time Napoleon was magnanimous enough to see that, owing to his age and the care of his children, he could not expect such a sacrifice.

So far, the Prince had done all that honour and affection could demand of him. But, unfortunately for his fame, instead of withdrawing into private life, he listened to the prayers of his wife, who keenly felt the loss of her title of "Serene Princess." It was at her desire that he continued to frequent the Bourbon court and actually accepted the captaincy of one of the new companies of royal guards. This and the fact that, as senior of the Marshals, Berthier had led his fellow Marshals to meet the King at Compiègne, caused the Prince of Wagram to be regarded as a traitor by Napoleon and the Imperialists. Moreover, the Prince Marshal now saw in Napoleon the disturber of the peace of Europe, so when the Emperor suddenly returned from Elba he withdrew from France, and retired to Bamberg, in his father-in-law's dominions.

It is commonly supposed that Berthier committed suicide, but the medical evidence shows that his fall was probably the result of giddiness arising from dyspepsia. It was on June 1st that the accident happened. He was watching a division of Russian troops passing through the town, and was much distressed by the sight, and heard to murmur, "My poor country!" Ever interested in soldiers, he got on a chair on the balcony before the nursery windows to get a better view of the troops, and while doing so lost his balance and fell to the ground.