The advent of Buenos Aires Province Governor Juan Manuel de Rosas led to Escribano's 1829 destitution as commander; though the intervention of an officer, Isidoro Suárez, forestalled a bloodbath.

Political wrangling and ongoing Indian raids had all but torn Junín down by the 1830s, however, and this prompted Governor Rosas to send the remaining settlers provisions and to subsidize crop farming in the neighbouring, high-yielding pampas fields.

Towards the end of his rule, Rosas appointed José Seguí, among the few Afro Argentines to achieve a commissioned officer's rank, to administer Junín, in 1851.

Rosas' 1852 overthrow resulted in the appointment of a justice of the peace, who firstly shared governing duties with the military commander.

The province designated the area as a county in 1864, and with nearly 2,000 inhabitants, Junín stops to be categorized as a "fort," and its first municipal master plan was laid out in 1865.

Junín's steady development over the following decades and setting amid lakes made it a well-known regional tourist destination.

The closure of much of Argentina's passenger-rail service during the 1990s was partly offset in Junín by the buying of local rail facilities by América Latina Logística, a São Paulo-based rail transport provider operating largely in Argentina, as well as by establishment of the Junín Railworks Cooperative.

The city features numerous cinemas, as well as prominent stage theatres such as the Teatro de la Ranchería (1971).

The public Dr. Abraham Piñeyro Emergency Hospital, opened in 1930, serves as the city's main health-care establishment; a new wing was added to the facility in 1997.