Key message The speed of infection of Quercus ilex by Phytophthora cinnamomi is influenced by the method of inoculation used, and structural changes in the host do not differ depending on whether primary or secondary roots are infected. Abstract This study aimed to elucidate the infection process of the invasive pathogen Phytophthora cinnamomi on primary and secondary roots of 2-month-old Quercus ilex seedlings. To test if different methods of inoculation lead to different changes in the host caused by the pathogen, the root system of plants was either immersed into a suspension of P. cinnamomi zoospores, or placed in direct contact with agar plugs colonized by P. cinnamomi mycelium. Histology of root sections obtained every 24 h for 10 days revealed similar changes in the structure of cells and tissues of the host irrespective of the inoculation method used. However, the immersion method resulted in a delay in the colonization of the host, different aerial symptoms, and the formation of different reproductive structures of the pathogen. Emerging secondary and tertiary roots and sites where secondary or tertiary roots were about to emerge were identified as main entry points. Hyphae in the xylem tissues were more frequently found in secondary than in primary roots, but in both types of roots the phloem was the most important pathway of colonization. For the first time in the interaction between Q. ilex and P. cinnamomi, transmission electron microscopy was used to describe degradation of the host cell walls, pit penetration and extrahaustorial matrix. Haustoria development during intracellular growth and hyphal aggregations (stromata) caused no damage to the host cell walls indicating hemibiotrophic parasitism.