At all costs, Weishaupt wished to keep the existence of the order secret from the Rosicrucians, who already had a considerable foothold in German Freemasonry. While clearly Protestant, the Rosicrucians were anything but anticlerical, were pro-monarchic, and held views clearly conflicting with the Illuminati vision of a rationalist state run by philosophers and scientists. The Rosicrucians were not above promoting their own brand of mysticism with fraudulent seances. A conflict became inevitable as the existence of the Illuminati became more evident, and as prominent Rosicrucians, and mystics with Rosicrucian sympathies, were actively recruited by Knigge and other over-enthusiastic helpers. Kolowrat was already a high ranking Rosicrucian, and the mystic Prince Charles of Hesse-Kassel had a very low opinion of the rationalist higher grades of the Illuminati.[20]

The Prussian Rosicrucians, under Johann Christoph von Wöllner, began a sustained attack on the Illuminati. Wöllner had a specially engineered room in which he convinced potential patrons of the effectiveness of Rosicrucian "magic", and his order had acquired effective control of the "Three Globes" and its attached lodges. Through this mouthpiece, the Illuminati were accused of atheism and revolutionary tendencies. In April 1783 Frederick the Great informed Charles of Hesse that the Berlin lodges had documents belonging to the Minervals or Illuminati which contained appalling material, and asked if he had heard of them. All Berlin masons were now warned against the order, which was now accused of Socinianism, and of using the liberal writings of Voltaire and others, alongside the tolerance of Freemasonry, to undermine all religion. In November 1783 the Three Globes described the Illuminati as a masonic sect which sought to undermine Christianity and turn Freemasonry into a political system. Their final anathema, in November 1784, refused to recognise any Illuminati as Freemasons.[20]

In Austria, the Illuminati were blamed for anti-religious pamphlets that had recently appeared. The Rosicrucians spied on Joseph von Sonnenfels and other suspected Illuminati, and their campaign of denunciation within Freemasonry completely shut down Illuminati recruitment in Tyrol.[20]

The Bavarian Illuminati, whose existence was already known to the Rosicrucians from an informant, were further betrayed by the reckless actions of Ferdinand Maria Baader, an Areopagite who now joined the Rosicrucians. Shortly after his admission it was made known to his superiors that he was one of the Illuminati, and he was informed that he could not be a member of both organisations. His letter of resignation stated that the Rosicrucians did not possess secret knowledge, and ignored the truly Illuminated, specifically identifying Lodge Theodore as an Illuminati Lodge.[20]