In the year 1844 his advice was asked by the king on the constitutional changes,—from absolutism to a representative government,—upon which Prussia, although in a first-rate financial military and administrative condition, found herself irresistibly constrained to enter. His advice, though studiously conservative, was considered of too sweeping a nature, and the king contented himself in 1847 with convoking an assembly composed of all members of the eight provincial diets of the monarchy, and clothed with scarcely any constitutional powers
On the question of church organization, also, the king and his friend were fated to disagree more strongly than they had expected. Bunsen's views had developed into a system essentially Presbyterian, though with an Episcopal headship. He held up the constitution of the Episcopal Church of America as, perhaps, the best type to follow, because it contained personal rule organically allied to the free power of the laity. He recommended these ideas to his countrymen as well as to his sovereign in a book entitled The Church of the Future, which has not been without influence in the church constitution now (1876) about to become law in Prussia.
The king's expectations of a quiet time for maturing his work of reconstruction in church and state were rudely broken in upon by the French Revolution of February 1848. Bunsen's warning voice had been raised in vain; the discontent of the educated classes helped to weaken the distracted councils of Frederick William IV., and, though a constitution was eventually promulgated, Prussian politics succumbed under the tutelage of the Austrian premier, Prince Schwarzenberg, in 1849 Bunsen's diplomatic labours were mainly directed to settle, as German commissioner, the dispute with Denmark about the duchies of Holstein and Schleswig, Great Britain having offered her mediation. In these duchies a strong agitation of several years standing had roused the German population, which occupies the whole of the former and part of the latter, to oppose the centralizing tendencies of the Danish Government. During the troubles of March 1848 they had taken up arms against Denmark and found assistance in Germany, then for the first time aspiring again to the position of a national power. This disturbance of the public peace of Europe was, however, regarded with so much disfavour by all powers, and secretly also by the sovereigns of Prussia and Austria, that the Danes obtained, in 1852, a European protocol, which reversed the political autonomy of the two duchies, and settled the crown of Denmark, after the death of the king and his son, upon Prince Christian of Glücksburg. It was the fate of Bunsen to be obliged to add his signature to this protocol, although it contained an abrogation of those “constitutional rights of Schleswig and Holstein,” upon which he had dilated in a Letter to Viscount Palmerston, printed in April 1848.
The unity of Germany was another of those wishes in which Bunsen and his royal patron had been one ever since the beginning of their acquaintance, and yet found themselves widely apart when the question came to be practically tested. The king sincerely aimed at the resuscitation of the venerable German empire, fancying that the leadership within the federation of sovereigns might be divided between Austria and Prussia, yet so as to leave a kind of ceremonial primacy to the former. Enlightened Germans, on the contrary, had then already arrived at the conviction that the leadership must be in Prussian hands. Austria, hampered as she is by the numerical preponderance of non-German populations, and the divergence of her interests from those of Germany, should, they thought, take her place within a wider federation. Gradually and almost imperceptibly did this truth work its way through time-honoured tradition. Bunsen was one of its most eloquent apostles, in his official correspondence as well as in pamphlets published in 1848. Several times he was sanguine enough to believe such a policy to be permanently grasped in Berlin, but the king's vacillating temper and his adherence to tradition refused to be wrought upon beyond the approval of half-measures. Thus the opportunity was lost, the potentiality of the Prussian military power neglected, and a gnawing disappointment left in the minds of the best patriots throughout Germany.
With small hopes, and with no other wish but to serve as long as possible a sovereign whose friendship and confidence had outlived their former agreement on matters of religion and policy, Bunsen continued in the thankless task of representing Prussia after the downfall of those proud hopes that had pictured forth a revival of the German nationality under Prussian leadership. His main object, pursued under every difficulty, and seized with energy on every favourable opportunity, was to dissociate the policy of Berlin from that of St Petersburg and Vienna, and to draw closer whatever bonds of common sentiment or interest existed between the English and German communities. He was not tardy, therefore, in advising his royal master in an anti-Russian sense when the Crimean war began. As had so often been the case, the king's understanding went along with much that Bunsen wrote, and hopes were entertained that a Prussian participation in the war, containing the threat of an invasion of the north-western frontier of Russia, would force that country into compliance with the demands of the Western powers. But traditional policy again prevailed, mixed with the king's unconquerable aversion to Napoleon III., and his growing mistrust of Lord Palmerston's political principles. The alliance of the Western powers was declined, Prussia preserved towards her Eastern neighbour what is technically called a “benevolent neutrality,” and the king accepted Bunsen's proffered resignation of his post as minister in London in April 1854.