The Concordat was denounced throughout the continent as treason to South American independence, and his relations with European diplomatic representatives were so cordial and frank that rumours of his willingness to accept a foreign protectorate or even annexation by Spain were rife in the other capitals. The publication of his personal correspondence with a French diplomatist raised such a storm against him that other countries plotted his overthrow, and the democrats of Colombia, victorious in the civil war of 1863, sent an army to the frontier, proclaiming that their purpose was "to liberate the brother democrats of Ecuador from the theocratic yoke of Professor Moreno." His army was defeated in the battle of Cuaspud, but he stood firm and his people showed no eagerness to accept Colombia's invitation and re-enter that confederacy. Her army was unable to follow up its advantage, and the danger quickly passed. When war broke out between Spain and Peru he, like the Emperor of Brazil, refused to follow Chile's example and take sides, against the mother country. In a word, his foreign policy was a selfish but intelligent opportunism, and he was not influenced by vague sentimental considerations and blind chauvinism.
In 1864 Urbina, with the countenance and assistance of Peru, invaded the southern province, Loja, but the insurrection was promptly crushed. Next year Moreno's term expired, and he named a disciple and friend to be president in his place, but his own political preponderance was so unquestioned and his prestige so enormous in the barracks, convents, and pulperias that he continued the real ruler of the country. His understudy did not please him and he demanded and received a resignation. The incumbent next selected proved insubordinate and had to be displaced by force. When Moreno declared himself provisional dictator the Guayaquil liberals undertook an armed resistance, but by 1869 he was firmly in the saddle once more. He kept his hold on the government, apparently becoming more securely entrenched each year in the love and confidence of the soldiery, the priests, and the common people. From the safety of exile the liberals wrote crushing pamphlets against him and his despotism, his favouritism toward the clergy, his steady, relentless policy of conservatism and reaction. But their attempts at insurrection were feeble and in 1875 he was re-elected as a matter of course. The liberals, hopeless of ending his domination constitutionally or by open war, had recourse to assassination. On the 6th of August a party of young Creoles deliberately killed him at midday on the principal square of Quito in the presence of the populace and the soldiery.