Across France Protestants responded to Condé's manifesto and the beginning of the first French War of Religion by seizing cities and taking control of territories. In total around 20 of the 60 largest cities in the kingdom would fall under rebel Protestant control. Among them Lyon, Tours, Amboise, Poitiers, Caen, Bayeux, Dieppe, Blois, Valence, Rouen, Angers, Le Havre, Grenoble, Auxerre, Beaugency, Montpellier, Mâcon and Le Mans. In the areas of Protestant domination iconoclasm and the seizure of churches was often undertaken. Protestant armies attempted to seize more cities that had not fallen to them. Among the leading Protestant commanders were the comte de Crussol (count of Crussol) who assumed a position of leadership in Languedoc and Dauphiné; the baron des Adrets in Dauphiné, the seigneur de Duras (lord of Duras) in Guyenne; the prince de Porcien in Champagne and the comte de Montgommery in Normandy.
This decentralised uprising would not be unopposed, and after initially being caught off guard by the sudden and dramatic nature of the conquests, local Catholic royalist commanders would begin to recapture the territories in their provinces. This included figures such as the seigneur de Monluc in Guyenne and Languedoc, the vicomte de Joyeuse (viscount of Joyeuse) in Languedoc; the comte de Sommerive in Provence; the duc d'Aumale in Normandy and the duc d'Ėtampes in Normandy. This would involve street battles to stop attempted Protestant seizures of cities (as in Toulouse and Bordeaux), the reduction of Protestant held cities (as with Poitiers and Rouen) and field battles (as in the defeat of the Protestant army of Duras by Monluc's army at Vergt in October.
By the end of 1562 the rebel Protestant presence in much of France had been successfully neutralised. However, in Languedoc and Dauphiné they remained entrenched under Crussol's leadership. Meanwhile Admiral Coligny oversaw the resurgence of their cause in Normandy shortly before the end of the war.
Picardy
The court moved to assure itself of its control over Picardy and its capital Amiens with the provinces governor in rebellion. Under the legal fiction that Condé was a prisoner of the rebels in Orléans, his brother the cardinal de Bourbon was made governor of Picardy in his stead. Bourbon entered Amiens on 27 July.
Amiens The Protestants had enjoyed great success in assuming influence in Amiens, and by 1562, seventeen of the twenty-four échevins (aldermen) were Protestant. During the ascension day procession, the échevins ensured it would be four of their number who carried the important châsse de Saint-Firmin (shrine of Saint-Firmin). A Protestant served as one of the cities schoolmasters. The remaining Catholic échevins were not willing to allow the Protestant success in the city to continue, and both the mayor and the prévôt (provost) were accused by them of being partisans of the Protestants as far as overseeing the prosecutions of the disorders of 7 and 8 December were concerned. It was further implied by the Catholics that they intended to launch a Protestant coup.
The Protestants of Amiens looked to the Protestant lieutenant-general of Picardy, the sieur de Sénarpont and Condé to defend their interests at court. Condé assures them of his protection and for the moment this proved more decisive than the coalition around the bishop of Amiens (which included the bishop of Nantes and Montmorency). Another appeal to the court by the radical Catholic faction was launched on 23 April with the dean of the local chapter travelling to court to get the keys removed from those who currently possess them as 'most of them were Protestants'. Those who travelled to the court highlighted the recent Protestant seizure of Rouen. The court was more sympathetic this time, Condé no longer present to represent the Protestant interests. On 5 May, the mayor and prévôt were replaced by the court, with the latter departing to join Condé in rebellion at Orléans. Within another month, Catherine appointed ten new échevins, all Catholic, giving the Catholics a municipal majority. This new Catholic majority quickly moves to neutralise their Protestant colleagues. The cardinal de Saint-Tryphon visited the city on 22 May to announce that it was the king's will that Protestant worship be proscribed in Amiens and other border cities. The Catholic échevins happily announced the expulsion of Protestant ministers in response. During July the abjuration of all Protestants in Amiens was decreed, with some who refuse to abjure choosing instead to leave the city. In the municipal elections of October a last minute addition to the electoral rules made Protestants ineligible from participating.
Montdidier The royalist recapture of Montdidier was undertaken by deception. Having promised that the Protestants of the city would be safeguarded, the royalist force butchered and expelled them.
Calais In May, the lieutenant-general of Picardy the sieur de Sénarpont made an abortive attempt to capture Calais.
Champagne Troyes Condé reached out to his nephew (who happened to also be in the capital when word of Wassy arrived), the Protestant - or at least Protestant sympathetic - governor of Champagne the duc de Nevers to source military and financial aid for the cause. Nevers had received the charge of governor of Champagne from his father in 1561, the latter having resigned it to him. Nevers passed the request he received on to the Protestant church of Troyes which was already in the process of arming its members.
In Troyes, close to Wassy, tensions were escalating severely between Protestants and Catholics with both accusing each other of interfering with the electoral process in the city. On 6 April, a representative of the duc de Guise, Esclavolles, passed through Troyes. He decided to preside over the election of the échevins which had been delayed, and excluded Protestants from the process. He further took charge in Troyes and demanded the keys. On 10 April he declared only Catholics would guard the gates. The Protestants dispatched a representative to Nevers to warn him that his authority was being usurped. On 12 April, Protestants seized two of the city gates, assaulting the gate keepers. Though there was bloodshed, it was comparatively bloodless in comparison with cities such as Toulouse. A captain on the way to join Condé passed through Troyes, and reported back from Orléans to the Protestants that Condé desired them to obey Nevers. Nevers arrived near Troyes on 19 April, with the intention of calming religious tensions in the city. He was aware that the Protestant community of Troyes had armed and wished to keep the situation under control. He wrote to the court that agitators from outside the town were attempting to escalate the situation. He was eventually able to persuade the Protestants of Troyes to stand down by promising to protect them. Nevers, now corresponding with the crown, adopted a posture of neutrality. Both religions were to guard the gates, and weapons were to be yielded to him. He hoped this would dispel fears of a new massacre of Wassy. However many Protestants refused to hand over their weapons and instead hid them. Protestant troops that had been raised initially at Nevers' request, slipped out of the city to join with Condé on 5 May. Nevers moved to have those who did not live in Troyes expelled from the city. Nevers was frustrated with the Protestant congregation of Troyes for their having sent troops to join with the Protestant rebels. He preferred the company of the Protestant bishop of Troyes Antonio Carraciolo to his co-religionists in the city.
In July, the Protestant prince de Porcien was in the area, and threatened an attack against Troyes, though it did not materialise. Fearful of a plague, Nevers retired from Troyes, leaving his more firmly Catholic subordinate des Bordes in charge. Nevers turned his attention to the nearby settlement of Châlons, where he had heard rumours of religious disorder. He was assured by the city council that while a Protestant preacher had been causing problems, the situation was now under control. In August repression against the local Protestant population began in Troyes.
On 24 August, des Bordes led an assault against the Protestant held town of Bar-sur-Seine. The Protestant cavalry guarding the town fled, and des Bordes oversaw a massacre of 140 Protestant inhabitants. Nevers' gendarme company participated in the killings, and according to Carroll the attack could not have happened without his approval. For Nevers, this was a military action against rebels, and therefore justified. According to the local contemporary historian Nicolas Pithou they tore out the heart of one of the Protestants and then took turns biting it. Those who survived were brought back to Troyes for trial, and then executed.
Bar-sur-Seine once more fell to Protestant forces in January 1563, this prompted a new round of persecutions and killing in Troyes.
Sens When the Protestants of Sens initially began pushing to receive churches, the mayor refused on the ground that the edict of Saint-Germain had not been registered. After it was registered he altered course to insisting the preachers of Sens speak out against the edict. On 29 March while returning to Courtenay from Sens where they had held a service a group of Protestants were attacked by Catholic boatmen. Local Protestant gentleman quickly intervened to protect them, but services were nevertheless suspended for the time being.
Before taking action, the Protestants looked to Nevers for leadership, but none came. While they stalled, the royalist Catholics of the city took the initiative. A militia was established (financed by the clergy), the gates secured and the artillery seized. A meeting was held among the Catholic grandees of Sens to decide how to proceed. It was decided to raze the Protestant church in Sens, on the day of the pilgrimage for St Savinien, when their numbers would be able to overpower the Protestants strong representation among the magistracy of the city. On the day the Catholic militia stood guard as the people of Sens tore down the church. Arrests of the Protestant leadership then began, and though chaotic did not descend into bloodshed in the morning. In the afternoon the Protestant captain returned and began preparing for a counter offensive, uniting with a band of co-religionists in a fortified house and then bursting out to attempt to push the Catholics back out of the neighbourhood. The captain attempted to make contact with a gendarmerie company of Coligny's. The Catholics brought up artillery and the captain was killed, with his unit dispersed. The general massacre then began. Canons invited peasants from the surrounding countryside into Sens to participate in the killing. According to the Protestants, 52 houses were pillaged and around 100 killed. Not all the killed were Protestants, with one Catholic magistrate being killed as he left mass. The parlement would investigate the incident but did not find anyone guilty.
Reims In Reims, there was relatively little risk of any Protestant uprising, the city would not be subject to any external attack or internal disorder during the war. Nevertheless, the baron de Cerny was appointed governor of the city in July. He ordered the council draw up a list of Protestants in the city, which was happily complied with by the city council. They provided Cerny a list of 25 names in September. No action was taken with the information on this list, as it was apparent the named were either not actually Protestants or presented no military threat to the city.
The duc de Nevers led an assault on a Protestant held château near Reims. He and his 1,600 soldiers tricked the garrison into emerging from the château and then slaughtered them.
Porcien's campaign