Joaquín was born in El Puerto de Santa María, Province of Cádiz. In 1999–2000 he started his senior career, appearing regularly for Real Betis B (after spending two years in the youth ranks) as it was eventually relegated from the Segunda División B. He moved to the first team the following season, making his professional debut on 3 September 2000 and having an immediate impact – 38 matches and three goals – as the Andalusians returned to La Liga after one year out.