Following the war, he returned to military law and eventually became the Judge Advocate General of the Army, a position he held from 1931 to his retirement from service in 1933.
During his time in office, Winship fought to have then-new minimum wage laws not apply to Puerto Rico, which would have doubled the hourly wage of 12.5 cents which was standard for sugar plantation workers. Although this decision was unpopular, when the new minimum-wage law was passed, nearly two-thirds of the island's textile factories were forced to close because they could not afford the increase.
Winship also was sharply critical of many of Secretary of the Interior Harold L. Ickes's policies toward the island. Relief spending for Puerto Rico was per capita far below either that of the mainland or Hawaii. This lack of spending contributed to the poverty of the island which itself led to some of the problems of unrest.
In the year 1934 there were major strikes on the island. In response, the United States appointed Gen. Blaton Winship as the governor. Col. Francis Riggs came with him and was given the post of Chief of Police. Riggs had formerly assisted Nicaragua's dictator Anastasio Somoza.
On (Oct. 24), 1935, at the University of Puerto Rico, Col. Riggs gave orders to fire on nationalist demonstrators. Ramón S. Pagan, Pedro Quiñones, Eduardo Rodríguez Vera, José Santiago Barea and a bystander were killed in what is now known as "The Massacre of Río Piedras". On February 23, 1936, the nationalists Hiram Rosado and Elias Beauchamp killed Col. Riggs in San Juan in retaliation for the massacre. Rosado and Beauchamp were both captured and executed at the police headquarters for their crime.
On Palm Sunday (March 21), 1937, Governor Winship cancelled a Nationalist parade which was to have taken place in Ponce, Puerto Rico only an hour before it was to have begun. When the march continued anyway, it was broken up by the police resulting in seventeen deaths and more than 200 wounded. 150 protesters were arrested. This event (later called the Masacre de Ponce or Ponce Massacre) sparked outrage even in Washington where Minnesota Representative John Bernard gave a speech denouncing the action to the United States House of Representatives on April 14th. A Grand Jury was convened to investigate the incident, but was closed without finding Governor Winship responsible. However, the prosecutors were appointed by the Governor and some have suggested that this may have contributed to a bias in Winship's favor. Following this investigation, the law which allowed public officials to be indicted was repealed, effectively granting Governor Winship immunity from further prosecution. A second panel, organized by the American Civil Liberties Union, also did not reach a conclusion which blamed Winship directly. (It criticized both the Nationalist militantism as well as the repression.)
Following those events, many of the leaders of the Nationalist party were put on trial for insurrection and after experiencing a hung jury and retried, six were sentenced to life in prison.
The following year, Governor Winship, moved the celebration of the 40th anniversary of the United States invasion of Puerto Rico to Ponce, instead of San Juan, Puerto Rico which had been traditional. This was seen by many as a direct response to the protests the prior year. During this celebration, on July 25 1938, Ángel Esteban Antongiorgi attempted to assassinate the Governor and managed to fire several shots before being killed by the police. (One police officer was also killed in the attempted assassination.)
Winship was removed from office on May 12 1939 after charges were filed against him by New York Congressman Vito Marcantonio. William D. Leahy was appointed by the President as his successor, though it would be several months before he could take that office. (During this time, José E. Colom would serve as Acting Governor.)
Ironically, Winship's term as Governor united many of the political factions of the island against him, leading to a strong win by the newly formed Popular Democratic Party in 1940.
Winship retired again in 1944. At 75, he was at that time the oldest Army officer on active duty.