The military history of the Acadians consisted primarily of militias made up of Acadian settlers who participated in wars against the English (the British after 1707) in coordination with the Wabanaki Confederacy (particularly the Mi'kmaw militias) and French royal forces. A number of Acadians provided military intelligence, sanctuary, and logistical support to the various resistance movements against British rule in Acadia, while other Acadians remained neutral in the contest between the Franco–Wabanaki Confederacy forces and the British. The Acadian militias managed to maintain an effective resistance movement for more than 75 years and through six wars before their eventual demise. According to Acadian historian Maurice Basque, the story of Evangeline continues to influence historic accounts of the expulsion, emphasising Acadians who remained neutral and de-emphasising those who joined resistance movements. While Acadian militias were briefly active during the American Revolutionary War, the militias were dormant throughout the nineteenth century. After confederation, Acadians eventually joined the Canadian War efforts in World War I and World War II. The most well-known colonial leaders of these militias were Joseph Broussard and Joseph-Nicolas Gautier.

Contest for supremacy in North America

King William's War (1688–1697)

The first war to influence the Acadians is now known as King William's War, and began in 1688. Much of the local conflict was orchestrated by the Governor of Acadia and Baron de St Castin, who raided Protestant villages along the Acadia-New England border at the Kennebec River in present-day Maine. The crews of the French privateer Pierre Maisonnat dit Baptiste were primarily Acadian.

The Acadians resisted during the Raid on Chignecto (1696). Colonel Benjamin Church and four hundred men (50 to 150 of whom were Indians, likely Iroquois) arrived offshore of Beaubassin on September 20. When they came ashore, the Acadians and Mi’kmaq opened fire on them. Church lost a lieutenant and several of his men.Church, p. 228 They managed to get ashore and surprise the Acadians. Many fled while one confronted Church with papers showing they had signed an oath of allegiance in 1690 to the English King. Church was unconvinced, especially after he discovered the proclamation heralding the French success at Pemaquid posted on the church door.

On October 18 Church and his troops arrived opposite the capital of Acadia, in the siege of Fort Nashwaak (1696), landed three cannons and assembled earthworks on the south bank of the Nashwaak River. Pierre Maisonnat dit Baptiste was there to defend the capital. Baptiste joined the Maliseet from Meductic for the duration of the siege. There was a fierce exchange of gun fire for two days, with the advantage going to the better sited French guns. The New Englanders were defeated, having suffered eight killed and seventeen wounded. The French lost one killed and two wounded.Roger Marsters. 2004. p. 34

Letters from an Acadian official censured and requested the removal of certain priests, called "do nothings", who took no part in the King William's War but attended strictly to their religious duties and were therefore suspected of favouring the British. After the siege of Pemaquid (1696), d'Iberville led a force of 124 Canadians, Acadians, Mi’kmaq and Abenaki in the Avalon Peninsula campaign. They destroyed almost every British settlement in Newfoundland, killed more than 100 British and captured many more. They deported almost 500 British colonists to Britain or France.

Queen Anne's War (1702–1713)

During Queen Anne's War, the members of the Wabanaki Confederacy from Acadia raided Protestant settlements along the Acadia/ New England border in present-day Maine in the Northeast Coast campaign (1703) . Mi’kmaq and Acadians resisted the New England retaliatory Raid on Grand Pré, Piziquid and Chignecto in 1704. The raid was led by Benjamin Church who was fired on by the local militia, who had gathered in the woods along the banks. According to Church, on the first day of the raid, the Acadians and Mi’kmaq "fired smartly at our forces".Benjamin Church, p. 273 Church had a small cannon on his boat, which he used to fire grape shot at the attackers on the shore, who withdrew, suffering one Mi’kmaw killed and several wounded. Church was unable to come ashore. Having withdrawn from the village, the next morning the Acadian and Mi’kmaw militia waited in the woods for Church and his men to arrive. At the break of day, the New Englanders again set off toward the village, under orders from Church to drive any resistance before them. The largest body of defenders fired on the raiders' right flank from behind trees and logs, but their fire was ineffective and they were driven off.

Conquest of Acadia and the Treaty of Utrecht Acadians joined the French privateer Pierre Maisonnat dit Baptiste as crew members in his victories over British vessels. Acadians also fought alongside the Confederacy and French soldiers to protect the capital in the siege of Port Royal (1707) and the final Conquest of Acadia. Acadians and the Wabanaki Confederacy were also successful in the Battle of Bloody Creek (1711). The victory at Bloody Creek rallied the local resistance, and prompted many of the Acadians who were nominally under British protection to withdraw to the north. Soon thereafter a force of some 600 warriors, including Acadians, Abenaki, and Mi’kmaq, under the leadership of Gaulin and Saint-Castin, gathered and blockaded Fort Anne. The defending garrison was small, but the attackers had no artillery and were thus unable to make an impression on the fort, and the fort was still accessible by sea. Gaulin went to Plaisance in Newfoundland for supplies and equipment to advance the siege; Governor Philippe Pastour de Costebelle provided supplies, but the ship had the misfortune to encounter a major British fleet and was captured. That same expedition abandoned its goal of attacking Quebec when eight of its ships were lost on the shores of the Saint Lawrence River; Governor Vetch, who had accompanied the expedition as a leader of the provincial militia, returned to Annapolis Royal with 200 provincial militia, after which the besiegers withdrew.

In the March 1713 Treaty of Utrecht, the French ceded "all Nova Scotia or Acadie, with its ancient boundaries, as also the city of Port Royal, now called Annapolis Royal, and all other things in those parts, which depend on the said lands and islands" to the British, but retained "the island called Cape Breton, as also all others, both in the mouth of the river of St. Lawrence, and in the gulph of the same name" with exception of the "island called Newfoundland with the adjacent islands," which "shall from this time forward belong of right wholly to Britain". For whatever reason, most Acadians refused to swear an oath of loyalty to Queen Anne or, later, King George. Thus were fifty years of nearly uninterrupted conflict to start, which were only to be punctuated by the expulsion of the Acadians.Parkman, p.135

Father Rale's War

Raid on Canso (1718) – The Squirrel Affair In the lead up to Father Rale's War, shortly after Cyprian Southack established himself at Shelburne, Nova Scotia (1715), the Mi'kmaq raided the station and burned it to the ground. In response, on 17–24 September 1718, Southack led a raid on Canso and Chedabucto (present-day community of Guysborough) in what became known as the Squirrel Affair. Southack laid siege for three days to Fort St. Louis at Chedabucto, which was defended primarily by Acadians under Acadian Bernard LaSonde. There were approximately 300 Acadians in the area.

On board HMS Squirrel, Smart held a number of Frenchmen, including Bernard Marres dit La Sonde, Captain Darguibes, the French fishing admiral, and Sieur Dominice, a Basque captain.

On 23 September, Smart and Southack pillaged Canso. The pillaged goods were then loaded onto several French ships that had been captured in the harbor. The following day, 24 September, Southack released the Acadian prisoners, with the exception of Bernard Marres dit La Sonde, onto the Canso Islands without any provisions or clothing.Campbell, p. 132 Others fled to Isle Madame and Petit-de-Grat, Nova Scotia.Robinson, p. 53; He seized two French ships, and encouraged Governor of Nova Scotia Richard Philipps to build Fort William Augustus at Canso.

During Father Rale's War, the Maliseet raided numerous New England vessels on the Bay of Fundy while the Mi’kmaq, helped by Acadians, raided Canso, Nova Scotia (1723). Much of the conflict of this war happened along the Acadia-New England border. A priest, Father Sebastian Rale and Wabanaki Confederacy members from Acadia also participated in the 1723, 1724 campaigns along the border against the British, who had long threatened to remove the Acadians because they would not take an oath of loyalty. Even during Father Le Loutre's War some twenty years later, the British talked of deporting the Acadians who would not swear loyalty to Britain. On 28 December 1720, in London, someone in the House of Lords said: "It seems as though the French in Nova Scotia will never be good British subjects to her Majesty ... This is why we believe that they should be expulsed as soon as the necessary forces, which will be sent to Nova Scotia, are ready."

King George's War

Siege of Annapolis Royal (1744) During King George's War, Abbe Jean-Louis Le Loutre led an insurrection consisting of Acadians and Mi’kmaq to recapture the capital in the siege of Annapolis Royal (1744). Acadian François Dupont Duvivier, who had led the Canso raid, led the second siege attempt against Fort Anne, with a force of 200 troops. Grand Pre had been the staging ground for the French and Mi’kmaw sieges of Annapolis Royal.Bates, p. 33, 41 Two Minas inhabitants, Armand Bigeau and Joseph LeBlanc dit Le Maigre, had traded with Louisbourg and assisted the supplying of Duvivier's forces by sea. Both transported Duvivier's force from Louisbourg to Baie Verte and then accompanied the expedition to Annapolis Royal and had served as scoutes and couriers. Duvivier arrived at Fort Anne on September 6, 1744. The first night he erected shelters. He used Joseph-Nicolas Gautier's house for his Headquarters.Bernard, p. 70 After both sieges, Gorham demanded to take control of Grand Pre. The British burned the dwellings of both Bigeau and 'Le Maigre' at Minas. In Annapolis, they burned the home of Gautier and imprisoning him and his family at Fort Anne until they escaped after 10 months. The British also burned the homes of Acadian pilots Paul Doucett and Charles Pelerain.

During the siege of 1745, the French officer Marin was required to withdraw from siege to protect Louisbourg from a British attack. He reported that upon hearing the news of Louisbourg and his own withdrawal from Annapolis Royal, the Acadians were "overpowered with grief from the apprehension of remaining in the disposition of the enemy". Marin had taken British prisoners at Annapolis and remained with them in the bay at Cobequid, where an Acadian said that the French soldiers should have "left their [the British] carcasses behind and brought their skins". The British officer also deemed there was enough evidence to hold Gautier's wife and Charles Raymond for collaborating with the siege.

After the siege of Louisbourg (1745), the Wabanaki Confederacy members from Acadia conducted a campaign against British civilians along the New England/ Acadia border. (Such campaigns were repeated in 1746 and 1747). After the first siege of Louisbourg (1745), the British deported thousands of "French Colonists" on Île-Royale to France.Johnston, A.J.B. Storied Shores. University College of Cape Breton Press. 2004., p. 70 There were Acadians among those deported.