So far as his governorship of Cuba was concerned, which is all in which we need here be interested, he had at this time reached the beginning of the end. The king decided to remove him from that office, though probably not so much to get rid of him there as to be able to keep his valuable talents continually employed nearer home. He had decided that Menendez was of more value to him as a captain of his fleet than as a civil administrator. Accordingly at the beginning of 1573 Alfonso de Caceres Ovando, a temporarily retired judge of the Supreme Court of Hispaniola, was commissioned to make the customary investigation of Menendez's administration. He was not, however, appointed to succeed Menendez as governor, but the latter was left for the time in office. This was a mark of the high favor in which Menendez was held by the king; and another token to the same effect was the provision that Menendez need not personally appear to answer any charges which might be made against him, but might, if he preferred, send an attorney in his stead. A third and perhaps still more notable indication of royal favor was in the fact that when Menendez elected not to appear in person, and not to send an attorney, but to ignore the whole investigation, he was not called to task, but was permitted to go without so much as a reprimand.
The investigation did not take place until November, 1573. Though brief it was thorough and searching. But it disclosed little that was to the discredit of Menendez, and nothing that was really serious. He seems to have been a somewhat gloomy and cruel fanatic, but a man of integrity and singular loyalty to his sovereign and his faith. He was zealous and energetic, but better fitted to command a ship or a fleet, or indeed an army, than to govern a state. Yet in both respects he failed. His chief concern in Cuba, as we have seen, was to promote her military defences; but he left La Fuerza incomplete, while the inestimable economic potentialities of the island were altogether neglected. So in Florida, he aimed at conquest with the sword and little else; and while he succeeded in holding the land against French assaults and intrigues, he did not develop there a colony comparable with those which were being developed elsewhere in the New World; and he had the mortification of seeing, in the closing years of his life, French, Dutch and British privateers swarming in defiance of him the seas which Spain claimed for her exclusive own.