In December 2019, the Mexican Football Federation announced the disaffiliation of Veracruz from Liga MX due to economic debts with first team players, its youth system, and the league.

Soon Veracruz won their second title, in the 1949–50 season, with the most overwhelming victory in the history of Mexican football, beating Monterrey, 14–0.

Years later Veracruz acquired famous players such as René Higuita, Braulio Luna, Adolfo Ríos, Luis Hernández, Fernando Arce, Alfredo Tena and others.

The Apertura 2004 season had been one of the best for Veracruz as they finished 1st place thanks to new signings such as Cuauhtémoc Blanco, Christian Giménez, Kléber Boas and others.

Veracruz was officially relegated from the Mexican Primera División league on the night of Friday May 2, 2008 in the final match of the regular season against Tecos UAG ending in a 0–0 draw.

With goals scored by José Valdivia, Luis de la Fuente and Raimundo Gonzalez, they ended a 26-year streak of the tournament being won by a club from Mexico City.

The 1950–51 tournament became the first losing year due to economical problems the club faced under the ownership of Miguel Alemán Valdez and governor of the state Marco Antonio Muñoz.

In 1961, thanks to a group of supporters, they established a patronage in which José Lajud Kuri was named president and so revived the club in order to take part in the 1961–62 Segunda División de México tournament.

Poza Rica and Veracruz had finished 2nd, 3rd and 4th (not counting Cruz Azul who had earned an automatic promotion after winning the tournament).

That year the club had a record of 10 wins, 8 draws, and 12 defeats; they scored 41 and allowed 44 for a total of 28 points and fishing 10 overall in the league.

One such was to buy the Ángeles de Puebla franchise which at the time was on sale due to the lack of supporters.

That game ended in a 3–5 win for the home team in a controversial match refereed by Javier Castellanos.

Botafogo ended up taking home the cup but the fans remember this tournament because the club beat Real Madrid, 4–2, with a goal by the Argentine Omar Palma.

The 1990s began with a group of players and a fan base which became known as La Tiburomaniam who cheer own fan favorite players Jorge Comas Adolfo Ríos, Joaquín Del Olmo, Octavio Becerril, Pascual Ramírez, José Luís González China under management of the Brazilian Edu.

In the 1994–95 tournament under the management of Anibal Ruiz who with a peculiar[clarification needed] defensive style of coaching made the fans lose interest in the club nonetheless the club qualified to play a knock-out match against its hated rival Puebla who advanced to the quarterfinals after a 1–1 draw moving on due to a better position in the league.

The club came close that year to winning the 1994–95 Copa México title after beating Irapuato, Estudiantes Tecos and Santos Laguna in that order facing Necaxa in the final match that took place in neutral ground in the Estadio Cuauhtémoc in the city of Puebla where the club fell 2–0.

In the 1996–97 the new owners signed José Mari Bakero who had just finished a long career with Spanish giant Barcelona along with key players from the Colombia national team Leonel Álvarez, Iván Valenciano, Alexis Mendoza mating important players and fan favorite goalkeeper Adolfo Ríos.

With the supports still hurt by the relegation at mid tournament Juan Manuel Alvarez was replaced by "El Turco" Aude coach who had much experience in the league and rallied the players reaching the semi-finals that year, losing the series to Venados de Yucatán.

A promotion series was played between Atlante who had the worst relegation percentage against the club that had gain the most points in the Primera A that been Veracruz.

The second match was played in the Estadio Azteca where Atlante defeated the Veracruz, 4–1, and remained in the top division.

In the Primera División de México Clausura 2008 the club once again had a bad year with a record of 4 wins, 5 draws and losing 8 for a total of 17 points finishing 16 in the league.

The club played in the Liga de Ascenso since the Apertura 2008 and came close several times but always coming short.

After enduring a 41-game winless run dating from September 2018 to October 2019, multiple reports of players not receiving payment, an in-game protest against Tigres UANL in the 2019 Apertura, where they conceded 3 goals in the first 8 minutes, and repeated discontent with owner Fidel Kurri, the FMF officially disaffiliated Veracruz from Liga MX following the 2019 Apertura.

[6] Subsequently, the team decided to redirect their application and began the procedure to join the Liga Premier de México.

[7] On May 23, 2022, the Club Deportivo Veracruz Facebook page published a statement stating that they had finally paid all their debts.