From 1805 to 1814, Bory followed the greater part of Napoleon's campaigns within the Grande Armée. In 1805, he took part in the campaign of Austria as captain of dragoons and was present at the Battle of Ulm (15-20 October 1805) and at the Battle of Austerlitz (2 December 1805). Captain Bory then spent two years in Prussia and Poland and fought at the Battle of Jena (14 October 1806) and at the Battle of Friedland (14 June 1807). He continued drawing military maps of Franconia and Swabia and during his visits to Bavaria, Vienna and Berlin, where he found his own works translated into German, he took the opportunity to meet several scientists including the botanists Nikolaus Joseph von Jacquin and Carl Ludwig Willdenow, who received him with open arms and presented him with valuable gifts. In October 1808, he served on the staff of Marshal Ney, which he soon left to be attached to Marshal Soult, Duke of Dalmatia, as aide-de-camp, in October 1809. Having been promoted to Major, Bory was mainly involved in military reconnaissance thanks to his skills in graphic work. From 1809 to 1813, he took part in the French campaign of Spain and distinguished himself at the Siege of Badajoz in the spring of 1811, at the Battle of Quebara and at the Battle of Albuera (16 May 1811). Events having placed him at the head of the troops that formed the garrison of Agen, he found himself commanding soldiers from his hometown for about two weeks. In May 1811, he became squadron leader and was then appointed Knight of the Legion of Honor and attained the rank of lieutenant colonel by the end of the year.