[2] The museum features an extensive permanent collection of over 6,500 pieces, and it encompasses more than 800 years of Puerto Rican, Latin American, Caribbean, and Latino art, includes pre-Columbian Taíno artifacts, traditional arts (such as Puerto Rican Santos de palo and Vejigante masks), twentieth-century drawings, paintings, sculptures and installations, as well as prints, photography, documentary films, and video.

The museum also sponsors numerous festivals and educational programs throughout the year including the annual Three Kings Day parade.

[9] However, Ortíz quickly redeveloped this project as the creation of a community museum that would be dedicated to Puerto Rican art and culture, and named it El Museo del Barrio.

[13] In 2009, El Museo celebrated its fortieth anniversary with public events, and the completion of an extensive renovation, which included an exhibition space for its permanent collection, a cafe, and a redesigned 4,500-square-foot courtyard.

[10] In 2015, El Museo recognized the gender gap in exclusion of women from museum exhibitions and committed to organizing a retrospective or major survey of works by a woman artist annually which would occupy the majority of the space in the museum and include public programming, publications and scholarship.

[15] In the early 2000s the museum experienced a significant increase in visitors, however remained confined to one floor in its building, which it shares with a school and a number of private organizations.

[18] After the failed relocation, El Museo opted to pursue a $15 million project to transform its outdoor courtyard into an open glass lobby, café and performance space, and to provide a suitable public "face" to the street on the model of the renovated Brooklyn Museum.

The renovation was spearheaded by local architect Gruzen Samton and completed at a cost of $35 million and added a shop and restaurant.

[20] Two forgotten artistic chandeliers were hung from the ceiling again and the refurbishments and re-opening were celebrated with a concert by legend and El Barrio native Eddie Palmieri, on February 20, 2021.