Bowyer was promoted to rear-admiral on 1 February 1793. He was sent to join the Channel Fleet under the now Admiral Howe, raising his flag in the ship of the line HMS "Prince" with Captain Cuthbert Collingwood as his flag captain, on 10 March. He transferred with Collingwood to the ship of the line HMS "Barfleur" when "Prince" was paid off in December 1793, staying in the Channel. On 1 June the fleet fought the battle of the Glorious First of June, with Bowyer being heavily engaged with the enemy from 29 May. Bowyer commanded the first division of the centre of the fleet during the battle, having under his command "Barfleur" and the ships of the line HMS "Invincible", HMS "Arrogant", HMS "Culloden", HMS "Theseus", and HMS "Gibraltar". At around 10 a.m. on 1 June itself Bowyer had his leg shot off by enemy fire, being caught by his flag captain as he fell. He was carried down to the ship's surgeon where the leg was amputated; Collingwood took over in his stead for the remainder of the battle. Bowyer officially left "Barfleur" in August.