Hungarian Diet
Returning to Arad, Mocioni helped establish there a National Culture and Enlightenment Association, presided upon by Prokopije Ivačković and Anton Mocioni. It received his collection of historical documents, and appointed him a delegate to Vienna, to thank the emperor for supporting Romanian culture. In 1863, his philanthropy expanded. He donated his only source of income, the revenue of Foeni, to the famine-stricken population of that village, and even ran into debt in his effort to provide for them. He was also interested in horse breeding, and one of his steeds became the ancestor of an equine string that populated much of Foeni.
For a while, the Romanians of Banat continued to plead with the emperor for Romanian self-rule in the Banat. One such petition, circulated in December 1863, also asked Franz Joseph to surround himself with Romanian advisers, including "Andrea de Mocioni, lord of Foeni", a man distinguished by "political, patriotic, and national virtues". As noted by historian Tudor-Radu Tiron, the restoration of Hungarian rule ultimately pushed the Mocionis back into Hungarian politics, which explains why Andrei, Anton and Gheorghe all took seats in the last Diet of Hungary (1865). Elected at Lugoj, Andrei served from December 14, 1865, and joined the Deák Party during his tenure; the other brothers were independent Romanian deputies. Alexandru also won a Rittberg seat in that legislature. Known as the theoretician of national liberalism, he was a main proponent of the Nationalities Bill, which, if adopted, would have set up autonomous units for the Romanians in Hungary.
By then, the Mocionis' contribution to the national cause was being recognized in the United Principalities, customarily known as the "Principality of Romania". From January 1865, he was an honorary member of the nationalist Bucovina Society. On April 22, 1866, the Romanian Regency appointed Andrei Mocioni a founding member of the Romanian Academy (or "Romanian Literary Society", as it was known at the time). He was inducted as a Banat representative, alongside Babeș—who, in 1883, wrote Mocioni's biography. From 1861, the Mocionis and Babeș had cooperated in countering Hungarian nationalist propaganda abroad, publicizing the Romanian point of view. According to Babeș, their effort was sabotaged by Abdolonyme Ubicini, István Türr, and Giovenale Vegezzi Ruscalla, who wanted a Hungarian–Romanian alliance against Austria; but also found backing from László Teleki of the Resolution Party. With his parallel career as a lawyer, Babeș also helped the Mocionis win back 5 million florins from their Hungarian debtors, and was thereafter their trusted adviser.
At the beginning of 1865, Count Zichy, the Aulic Chancellor for Hungary, proposed to Anton and Andrei Mocioni that the Mocioni family be elevated to the rank of Counts of Hungary and inducted into the House of Magnates. Zichy tasked Vincențiu Babeș with delivering the news to them. Upon finding out, both brothers refused. Andrei told him, "Tell him to at least restore my peace of mind, if he cannot restore the trust that those above have stolen from me!", while Anton said: "Those above take us for wretches or fools; and little do they know that I would be ashamed to appear among people bearing the title of Count, so long as the miserable state of today's Romanian nation endures!"
Later in 1866, echoes of Mocioni's "Captaincy" project were discernible in the radical proposal advanced in the Diet by Babeș, Hodoșiu, and Sigismund Popoviciu: it recognized subjection to the Hungarian crown and government, but sought to redefine Hungary on the basis of ethnic federalism and corporatism. These efforts also failed. By September 1866, Mocioni and Babeș began speaking out in the Diet about the wish of Austrian Romanians to be united with the Principality of Romania.
The 1866–1867 interval was a great disappointment for all factions within the Romanian caucus: the return of Hungarian nationalism was unopposed following the Austro-Prussian War, and the Ausgleich of 1867 created Austria-Hungary, attaching most Romanian-inhabited to the Lands of the Crown of Saint Stephen. Mocioni was especially affected by the outcome. In the months following the new arrangement, Mocioni and Babeș participated in the drafting of another protest, also signed by the Diet's Serb, Slovak and "Ruthenian" deputies. The resolution, which demanded guarantees for the minorities, was supposed to be read by Mocioni. He stepped down to make way for a more popular deputy, the Serb Milán Manojlovics. Brother Anton Mocioni, alongside Serbs Stevan Branovački and Svetozar Miletić, continued to back the campaign, proposing to divide Hungary into six ethnic-based provinces.
Andrei Mocioni's dissapointment with the Austro-Hungarian compromise dissilusioned him from Habsburg loyalism. On 26 February 1867, Mocioni visited Lajos Kossuth - his former enemy - in Turin. In that meeting, he tried to forge an alliance between the radical anti-Habsburg Hungarian revolutionaries and the ethnic minorities of Hungary against th Habsburgs. He told Kossuth that "the Romanians of Transylvania and Hungary want an independent Romania. In order for that to happen, Hungary must also become independent from Austria and to stop being Vienna's pawn. An united Austro-Hungarian Empire will always want a weak Romania, while an independent Hungary, in order to have good relations with Romania, must give its ethnic Romanians national rights". The meeting had no results, as Kossuth did not return to Hungary. Historian Ioan Dimitrie Suciu argues that this meeting showed that Mocioni envisioned a future Romanian state that would also include Transylvania and Banat.