Immediately after retiring, César began coaching his only club, being relegated from division two in his third season and promoting immediately back. In 2004, he signed with another team in the second tier, Gimnàstic de Tarragona.
Luis César led Nàstic to La Liga in the 2005–06 campaign, with the Catalans returning to the tournament after 56 years. On 26 November 2006, however, after a 2–3 home loss against RCD Mallorca, with the side having only totalled five points in 12 rounds, he was fired.
For 2007–08, César signed for Polideportivo Ejido in the second division, but did not finish the season once more, being sacked after the 21st matchday (out of 42), with Fernando Castro Santos taking his place as the Andalusians were relegated after a seven-year stay in the competition. On 6 March 2010, months after a move to UD Las Palmas was eventually aborted, he returned to Gimnàstic after the dismissal of César Ferrando, with the team eventually finishing in 18th position – the first place above the relegation zone – just one point ahead of Cádiz CF.
On 6 December 2010, following a 1–2 home loss against Villarreal CF B, Luis César was relieved of his duties at Gimnàstic, as the team ranked 22nd and last with just two wins in 15 games. In the 2011–12 campaign he was one of two managers in charge of CD Alcoyano, who were finally relegated from the second level.
Luis César was appointed at division three club Albacete Balompié on 20 March 2013, leading it to promotion at the end of his first full season. He was fired on 12 March 2016, and continued to work in the second tier with CD Lugo, Real Valladolid and CD Tenerife.[11
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