Juan has taught and held leadership roles at several institutions. His first permanent position was at Goldsmiths between 2000 and 2008, where he started as a part time Tutor progressing to be a full time Senior Tutor on the BA Fine Art programme and also acting as the Departmental Access and Recruitment Tutor. Between 2008 and 2014 he worked at Liverpool School of Art and Design, Liverpool John Moores University, first as Head of Department for Art and then as Director of School.

While at Liverpool, Juan developed innovative and sustainable patterns of cooperation between the University and cultural organisations in the city, co-founding joint research centres, including the Exhibition Research Centre, and establishing tenured posts that operated across the organisations. These posts continue to operate, enriching the collaboration across academia and industry and providing a really distinctive and rich set of opportunities for the city. Some of this work was funded by the University while other aspects were funded by the Arts Council, from whom Cruz raised funds to develop projects relating to the employability of graduates in the city.

In 2014 Juan joined the Royal College of Art as a Professor and Dean of Fine Art. He led the amalgamation of the School of Fine Art with the School of Humanities and became Dean of Arts & Humanities in 2017, and oversaw significant growth in the PGT and PGR communities. During his time at the RCA Juan held the role of Show Director and developed a broad range of public programming initiatives, including exhibitions and public events. He was also involved in the selection of architects, planning and fund raising efforts for the Battersea South development of a new Herzog & deMeuron building, scheduled to open in 2021.

Juan is a specialist in research based in art practice and is Deputy Chair of REF2021 Sub Panel 34: Art & Design History, Theory and Practice, having been a panel member in 2014. He was also a member of PBRF Creative and Performing Arts Panel 2018 (New Zealand Research Assessment Exercise).

Juan remains active in his own research, generating a diverse range of outputs. Exhibitions of his works are, more often than not, responsive to the particularities of the context where they are installed, but the work itself is almost always based on personal content. Juan writes autobiographical narratives and shorter descriptive texts, which he has deployed through videos, installations, typescripts, prints and performances; he has also worked with translation, performing several oral translations of works from Spanish literature, including Don Quijote, into English and, more recently, of American art magazine Artforum into Spanish. In 2006 ‘Juan Cruz A translation of Niebla (Fog) by Miguel de Unamuno’ was published by Forma and in 2007 another translated work, ‘SEDA, an Interesting Story’ was included in ‘The Alpine Fantasy of Victor B. and Other Stories’, Serpent’s Tail, London.

In 2017 Juan held a major museum exhibition of his work at MUSAC, Spain, titled Catalogue: it will seem a dream, which was accompanied by a 316 page book collecting numerous writings and published by Occasional Papers. More recently, in 2018, he exhibited an ongoing series of videos titled ‘I don’t know what I’m doing but I’m trying very hard’ at Matt’s Gallery, London.

In 2019 Juan was awarded an AHRC UK/China Creative Industries award for a project titled ‘Art Fair Innovations’ to develop better links and the enhanced used of digital media between the commercial art worlds in China and the UK.