As the leading ship of the line, Neptuno was initially isolated from the main fighting, though she joined in an attempt later in the day to come to the aid of Villeneuve's flagship.

She was towed towards a friendly port but, already badly damaged in the battle, was caught up in the powerful storm that struck the area and ran aground.

[2][3] There then followed a period of fitting out and carrying out sea trials during 1796, after which she was assigned to the Spanish Mediterranean fleet at Cartagena under Admiral José de Córdoba y Ramos.

[2] Neptuno put to sea on 1 February 1797 with the rest of Córdoba's fleet, consisting of 27 ships of the line, twelve frigates, one brig and several smaller craft.

[2] Córdoba had orders to deliver a number of gunboats to Algeciras to support the bombardment of Gibraltar, safely escort a convoy of four urcas carrying mercury from Málaga to Cadiz, and then sail to Brest to link up with the French.

[4] The first part of the operation went smoothly, and Neptuno was detached with the 74-gun ships Bahama and Terrible, the 34-gun Nuestra Señora de Guadalupe to take the gunboats into Algeciras.

[4] As they approached Cadiz on 14 February his fleet was tracked down off Cape St Vincent by a British force under Sir John Jervis.

[5] He sailed again on 9 August, taking the Spanish ships he had found in those ports, including Neptuno, with him, hoping to rendezvous with the French Rochefort squadron under Zacharie Allemand.

[6][7] After spending several months there, watched by the blockading British fleet under Nelson, Villeneuve decided to put to sea in mid-October.

[2][3] She was ahead of the 74-gun French Scipion, and formed part of the squadron under Rear-Admiral Pierre Dumanoir le Pelley, which had previously been intended as the rear of the fleet.

[2] Initially isolated by the British strike at the centre and rear of the combined fleet's line, Neptuno was ordered to hug the wind to allow the other ships to get to their stations.

[2] Neptuno was fired upon by the 64-gun HMS Africa, which had arrived late to the battle and sailed southwards parallel down the line, exchanging broadsides with the ships of the fleet.

[2] At 2 pm Dumanoir brought the van around and headed south to support the beleaguered centre, trying to fight his way through to Villeneuve's flagship, the 80-gun Bucentaure.

[10] Valdés was undergoing treatment in the cockpit, so First Lieutenant Antonio Miranda went aboard Minotaur and submitted his sword to her captain, Charles Mansfield.

[10] The battered mainmast collapsed on 22 October, smashing through the captain's cabins below the poop, crushing to death Spanish paymaster Diego de Soto as he slept, and killing one of the British prize crew.

[10] On 23 October French Captain Julien Cosmao and Commodore Enrique MacDonell[12] made a sortie from Cadiz with some of the more seaworthy ships that had escaped the battle, in an attempt to retake some of the captured prizes.

While Cornélie, Hortense, Thémis and Rhin harassed the British, Hermione took Neptuno in tow, while the Spanish crew rose up and took back their ship.