Of all the divisions of troops there remained only two to be vanquished, those of Hegau-Black Forest and of Allgaeu.Archduke Ferdinand had tried intrigues with both.In the same way as Margrave Casimir and other princes tried to utilise the insurrection to annex the church territories and principalities, so Ferdinand wished to utilise it to strengthen the power of the House of Austria.He had negotiated with the Allgaeu commander, Walter Bach, and with the Hegau commander, Hans Mueller, with the aim of inducing the peasants to declare their adherence to Austria, but, both chiefs being venal, their influence with the troops went only so far that the Allgaeu troop concluded an armistice with the Archbishop and observed neutrality towards Austria.
Retreating from the Wuerttemberg region, the peasants of Hegau destroyed a number of castles, and received reinforcements from the provinces of the Margraviate of Baden.On May 13 they marched towards Freiburg; on May 18 they bombarded it, and on May 23, the city having capitulated, they entered it with flying colours.From there they moved towards Stockach and Radolfzell, and waged a prolonged petty war against the garrisons of those cities.The latter, together with the nobility and other surrounding cities, appealed to the Lake peasants for help in accordance with the Weingarten agreement.The former rebels of the Lake Troop rose, 5,000 strong, against their former allies.So potent was the narrow-mindedness of the peasants who were confined to their local horizon, that only 600 refused to fight and expressed a desire to join the Hegau peasants, for which they were slaughtered.The Hegau peasants, themselves, persuaded by Hans Mueller of Bulgenbach, who bad sold himself to the enemy, lifted their siege, and Hans Mueller having run away, most of them dispersed forthwith.The remaining ones entrenched themselves on the Hilzingen Steep, where, on July 16, they were beaten and annihilated by the troops that had in the meantime become free of other engagements.The Swiss cities negotiated an agreement with the Hegau peasants, which, however, did not prevent the other side from capturing and murdering Hans Mueller, his Laufenburg betrayal notwithstanding.
In Breisgau, the city of Freiburg also deserted the peasant Union (July 17) and sent troops against it, but because of the weakness of the fighting forces of the princes, here as elsewhere, an agreement was reached (September 18), which also included Sundgau.The eight groups of the Black Forest and the Klettgau peasants, who were not yet disarmed, were again driven to an uprising by the tyranny of Count von Sulz, and were repulsed in October.
On November 13, the Black Forest peasants were forced into an agreement, and on December 6, Walzhut, the last bulwark of the insurrection in the Upper Rhine, fell.
The Allgaeu peasants had, after the departure of Truchsess, renewed their campaign against the monasteries and castles and were using repressive measures in retaliation for the devastations caused by the Union army.