Born in Cáceres, Extremadura, Morientes moved to Sonseca, Province of Toledo, at the age of four. He began his professional career at Albacete Balompié, making his La Liga debut on 7 November 1993 as a 75th-minute substitute for Alejandro in a 2–3 loss against CD Tenerife at the Estadio Carlos Belmonte, and he made one more appearance that season, also from the bench.

On 23 October 1994, soon after coming on as a first-half replacement for Alberto Monteagudo, Morientes scored his first professional goal, opening a 2–0 home win over Racing de Santander. He got his first start a week later in a 1–5 loss at RCD Español, and finished the campaign with a total of five goals in 20 league games; additionally, he found the net in each leg of a 3–2 aggregate win over holders Real Zaragoza in the last-16 of the Copa del Rey.

Morientes transferred to Zaragoza in 1995, where he spent another two seasons, often being partnered up front by Dani, a Real Madrid youth graduate. He made his debut on 9 September away to Real Betis, scoring the team’s goal after 48 minutes but being sent off seven minutes later for striking Jaime. On 10 January of the following year, he scored his first professional hat-trick in a 3–2 win at Athletic Bilbao for the domestic cup; his first such feat in the league followed on 3 February in a 4–1 win over Valencia CF at La Romareda, and eight days later he scored the first goal at SD Compostela and also received his marching orders with his team winning 2–1 (eventual 2–3 defeat).