Morientes was born in Cilleros, a small town in the western province of Cáceres, Spain. He began his top-flight career at Albacete in 1993 at the age of 17. He spent two seasons at the club, scoring five goals in 22 appearances (9 starts and 13 substitute appearances). Morientes transferred to Real Zaragoza in 1995, where he spent another two seasons. He scored goals regularly, and in his time at Zaragoza managed 30 goals in 66 appearances for the club.

Real Madrid

Morientes' performances for Zaragoza caught the eye of Spanish giants Real Madrid. He transferred to the club in the summer of 1997 for approximately €6.6 million. Morientes made 33 appearances for the club, scoring 12 goals. He formed a successful strike partnership with Raúl González. Real Madrid also won the Champions League in this season. In the 1998/99 season, he performed very well, scoring 19 goals in the league and 25 goals in 38 appearances overall. He continued to perform well in the 1999-2000 season, scoring 19 goals and finishing as Real's top scorer in a year where he also helped Real to their second Champions League title in three seasons, scoring in the 3-0 win over Valencia in an all-Spanish final. In the next season, Morientes won the first of two La Liga titles with Real Madrid, scoring 10 goals overall which included four in eight appearances in the Champions League as Real lost in the semifinals to eventual winners Bayern Munich. He missed the tail-end of the La Liga season due to injury.

In the 2001/02 season in La Liga, Real failed to win the league, losing out to Valencia. However, Morientes continued his scoring form, scoring 18 league goals in only 25 starts, with six substitute appearances. He also scored five goals in Real's 7-0 demolition of Las Palmas, missing out on a double hattrick after missing from the spot late in the match. He finished second in the topscorers list for the season, tied with Patrick Kluivert and behind Diego Tristán. Real were successful in winning the Champions League after beating Bayer Leverkusen. Morientes played in the final and received a third Champions League winners medal.

In the summer of 2002, Real Madrid signed Brazilian superstar Ronaldo from Inter Milan. This fuelled rumours that Morientes would soon be leaving the club, with Barcelona and Tottenham Hotspur reportedly interested. Barcelona were reportedly on the verge of signing Morientes for around €22 million, but the move fell through due to Barca's reluctance to match Morientes' wage demands. Eventually, Morientes decided to stay at Madrid, but as predicted he did not feature as much in the side after the arrival of Ronaldo, who was preferred to Morientes in the starting lineup along with Raul. Morientes also had a highly publicised spat with the then Real manager Vicente Del Bosque during a Champions League match against Borussia Dortmund in early 2003. In the January transfer window, despite continuous rumours of moves to Tottenham, Real Zaragoza,A.S. Roma and A.C. Milan, Morientes remained at the club for the remainder of the season. Real would go on to win the league and Morientes earned his second La Liga medal, making a total of 15 appearances (with three starts) and scoring five goals.

It was now clear that Morientes was not part of the first team at Real Madrid. At the start of the 2003-04 season, after extensive but ultimately unsuccessful negotiations regarding a loan deal with Germany's Schalke 04, he was loaned to Ligue 1 side AS Monaco. Here, he performed very well, scoring 10 goals in 28 appearances in the league. However, it was in the Champions League that he really made an impact. Monaco reached the final of the competition, eventually losing in the final to FC Porto. Morientes finished as the top scorer, scoring nine goals. Ironically, Monaco met Real Madrid in the quarter-finals. Morientes scored a vital away goal for Monaco in the first leg, which Real Madrid won 4-2. He was applauded by the Real Madrid fans after he scored. In the second leg, he scored again as Monaco won 3-1, taking the aggregate score to 5-5. Monaco went through on away goals. He also scored in their semifinal victory over Chelsea, but could not prevent Monaco from losing 0-3 in the final to Porto, played, ironically, at the Arena AufSchalke in Gelsenkirchen, Germany. Morientes' form resulted in him winning the 2004 European Striker of the Year award.

After returning to Real Madrid at the start of the 2004/05 season, Morientes' hopes of forcing his way into the Real squad were further dampened with the arrival of Michael Owen from Liverpool. It was clear that Morientes was surplus to Real's requirements. As a result, he was transferred to Liverpool in January 2005 for a fee of £6.3m, after making only 13 substitute appearances for Real in the first half of the season.

During his time at Real Madrid, Morientes made a total of 182 league appearances, with 112 starts and 70 appearances as a substitute. He scored 72 league goals.

Liverpool

He made his debut for the club against rivals Manchester United and scored his first Liverpool goal on February 1, 2005 against Charlton. He was cup-tied for Liverpool's Champions League campaign and did not feature in their victory against AC Milan in the final of the competition.

Although Morientes came to Liverpool with a very good reputation, his transfer to Merseyside was followed by a large dip in form. He scored only three goals in the 2004-05 season. He was often played in a deep-lying striker's position instead of his favoured target man role, and failed to adapt to this new role, as well as the faster style of the Premiership. At the end of the 2005-06 season, he was sold to Valencia. During his time at Liverpool, he managed only 12 goals in 61 appearances, although he was part of the squad that won the 2006 FA Cup.