In July 1939, a group of young students from Colegio Nacional Bolívar gathered to form an independent sporting club, and shortly afterwards entered a minor tournament under the name 'Independiente'.

With such class players as Peruvian all-time great Germán Leguía, fellow countryman and international Juan Martín Caballero, Uruguayan playmaker Rodolfo Abalde and such leading Ecuadorian players as Geovanny Mera, Jorge Alvear, Angel Buenaño, Juan Carlos Suárez, Ricardo Porras and Milton Rodríguez; the team became serious title contenders in the late 1980s and, although never becoming champions, they were recognized as a great national footballing side that would on several occasions maul the country's greatest teams including Barcelona and Liga, and their classic rivals, Técnico Universitario.

At this time they had a good group of players including Daniel Garrido, John Ordoñez, Lino Sánchez and Héctor Lautaro Chiriboga, that would remain for the next season.

However, the Ecuadorian economic crisis of 1999 and 2000 was a painful hit for the club, and added to that, their key player, Lino Sánchez's, suffered an injury in 2000 that would finish his career.

2004 was an unsatisfactory year, because, although having good players in Cristian Mora and Oscar Monge and others, it became difficult for the team to reach the last 6's group and be in contention for the title and the expenditure for appointing renowned coach Dussan Draskovic did not succeed as well as was hoped.

After he left, they signed Argentinian, Raúl Urquiza, who did a much better job on the last stretch of the tournament, lining up players that were overlooked by the former coach and contributing to the development of more effective plays, which reached its peak at Ibarra's Olympic Stadium on 3 October 2007, when Macara's offensive power burst in full force, scoring 4 goals in the first half and receiving just 1 in the second.

With a large number of fans cheering for them on 7 October 2007 and confirming their good moment, they defeated Emelec 2–0 and Macará had for the second year in a row, kept its place on the premier section of Ecuador's Campeonato Nacional.

They saw three of their best players leave the club, Luis Miguel Garcés went to cash-rich Barcelona, Mariano Mina transferred to Deportivo Cuenca and Christian Botero switched to Universidad Católica, where he played for a few months before going into retirement (and swiftly returning to Macará as an academy coach).

The team struggled for the major part of the first semester, which meant repeated fates for successively fired coaches De La Pava and Argentinian Jorge García.

The majors sponsor are Universidad Tecnológica Indoamérica, local footwear company Venus, Makrotubo, L. Gilbert, Hotel Casino Emperador and Ecuavisa, which also broadcasts the team's home games.