Founded in 1954, after a previous Guadix CF was already dissolved in the city, the club initially only lasted six seasons active. In 1962, UD Accitana was founded, but folded two years later. In 1969, Club Amigos del Deporte was created, later adopting the name Guadix CF.
After years floating between the lower divisions, Guadix club came to national recognition during the 2000–01 Copa del Rey, after knocking out Valencia CF in the round of 32 on penalties; in the following round, however, it was eliminated by Granada CF also from the spot.
In 2005, Guadix sold his spot in the Tercera División to Granada Atlético CF, whilst at the same time AD Íllora (from Íllora) was named Guadix CD. In 2008, Guadix CD was renamed to the actual Guadix CF, inheriting the old club's history.