He has directed sixteen films since 2005. He won the award for Best Director for his film Kinatay at the 62nd Cannes Film Festival. His 2009 film Lola won the award for Best Film at the 6th Dubai International Film Festival. His 2012 film Captive was shown in competition at the 62nd Berlin International Film Festival in February 2012.
His 2012 film Thy Womb competed for the Golden Lion at the 69th Venice International Film Festival. and earned Mendoza the award for Achievement in Directing at the Asia Pacific Screen Awards in 2012. His film Taklub has been selected to be screened in the Un Certain Regard section at the 2015 Cannes Film Festival.
On 25 July 2016, he directed the first State of the Nation Address of President Rodrigo Duterte. Mendoza was again attached to direct Duterte's second State of the Nation Address on 24 July 2017.