The position of St Domingue in 1788 was unclear because in at least theory, two thirds of the island belonged to the French and was one of the their largest remaining colonies. However the revolution in France was causing great concern to both Britain and Spain. In addition, the revolutionary government could scarcely maintain a presence on the island. A position that also held for every other French overseas colony, making them easy for their enemies to conquer.
Following the Revolution, Spain gave refuge to the French nobility, including former King Louis XVI, who set up a strong movement to ask Spain to bring control of Santo Domingo under the Bourbon flag. While Spain did not formally recognize the revolutionary government, it did not seek to confront the French so directly, but with Britain taking control of other French colonies in Africa and the Caribbean, the Spanish finally decided to take over Santo Domingo.
By June 1791, the Spanish had taken effective control of the island including Port du Prince, without any opposition from the British. This, among other issues in the Mediterranean and on the Spanish-French border, led the French revolutionary government to declare war to Spain.
France advanced on Barcelona during the winter to 1792. While the French fought the war in Spain on land or near to the Mediterranean coast, the Spanish attempted to grab as many of French colonies as their British allies allowed. However, by the spring of 1792, Spain had freed Barcelona from French occupation and a first treaty was signed between Spain and revolutionary France which recognized Spanish control over Santo Domingo. All other French colonies would be returned to France and some border adjustments were made to the European borders which mostly favored France.
Spain also agreed to recognize the property rights of French subjects in Santo Domingo. In addition, the Spanish government persuaded French refugees to go to Santo Domingo and claim any unused land. However most of the former French nobles migrating to the Americas chose Florida over Santo Domingo.
In 1797, a slave revolt started in western Santo Domingo which the Spanish had to use a large part of their resources to crush. The threat or reality of slave rebellions led many Frenchmen to move to Florida or to return to Europe. The rebellion was practically crushed by late 1799.
After the war against the U. S. of A., the Spanish were still hunting for rebels in Santo Domingo, but most of the French institutions in the island had disappeared.