The Supreme Court was composed of a presiding officer, two judges and a judge-advocate. Each of the states of the Republic was divided into districts, and a civil and criminal judge as well as an attorney for the Commonwealth were appointed for each district.
Each state was to be ruled by a Civil Governor, and each district by a Lieutenant-Governor, while the districts were divided into prefects and sub-prefects, each with its appropriate ruler. The officers in question were in every case to be elected by popular suffrage.
A chronological enumeration of the laws enacted by the Congress during 1869 is not only pertinent, but it divulges their evident intention to administer the government of the island, should they obtain the power to do so, along the most humane and enlightened lines.
On May 11, 1869, an amnesty was granted to all political prisoners, who had not already been sentenced.
On June 4, much needed provisions for civil marriages, and regulations concerning the same, were enacted.
On June 7, the commerce of the Republic was declared free to all nations.
The enactment of June 15, while a customary proceeding, would have a touch of irony connected with it, if it were not almost pathetic, as revealing the sturdy belief of these officials of the young Republic in the ultimate triumph of their cause. It was an authorization of the issue of $2,000,700 of legal tender paper money, to be redeemed by the Republic in coin, at par, when circumstances enabled them to do so—that is when they had conquered the enemy and established their Republic on a lasting basis. The bills thus issued had already reached the officers of the Republic, having been engraved in New York, and sent to Cuba by the New York Junta.
On July 9, the army was definitely organized, and this organization remained in force until the capture and death of General Quesada. It was as follows:
| Commander-in-Chief | General Manuel Quesada |
| Chief-of-Staff | General Thomas Jordan |
| Chief of Artillery | Major Beauvilliers |
| Brigadier-Major of Orders | Major Bernabe Varona |
| Sanitary Department | Adolfo Varona |