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Boosted by the naval victory of Naples, the French prepared a naval expedition to relieve Malta and Egypt, collect French ships at Malta and destroy the Royal Navy in the Mediterranean with Spanish support. The relief would occur on 10 September 1799 and it would relieve Malta for several weeks, the Egyptian part of the relief effort being temporarily cancelled due to poor performance in the Italian campaign. When the convoy reached Malta on 20 September 1799, Malta was successfully resupplied, the remnants of the British Mediterranean Fleet being destroyed without foreign support. Also, 3 undamaged by battle ships of the line and the same number of frigates were brought from Malta to Toulon to reinforce the French navy at Toulon with the Genereux.

Meanwhile, France suffered from various defeats on land, which led to Napoleon's 9 November 1799 coup. In the Netherlands, mutiny and a coastal invasion by Britain and Russia captured the remnants of the Batavian Navy after Camperdown. Also, the return of Napoleon would reinvigorate French morale and lead France to victory over Austria at Marengo in June 1800. However, Egypt and Malta had to be resupplied. The defeat at Naples didn't lead to further British cooperation with Russia and the Ottomans due to suspicions.

Nevertheless, the Russians and Ottomans would continue to dominate the Eastern Mediterranean. Egypt would remain blockaded due to the lack of French resupply efforts.