Olive cultivation is a key agricultural activity in Spain, primarily for producing oil. The extraction process of olive oil from the drupe yields a by-product known as ‘alperujo’, which can be composted and utilized as fertilizer. This research examines the impact of composted ‘alperujo’ on arthropod assemblages in the tree canopy, comparing it to mineral fertilization over the years 2021 and 2022. The study was conducted in two olive groves with different management systems (superintensive and traditional). Two types of sampling methods were used for the canopy: visual survey and sweep net. Under superintensive management, the presence and damage of Eriophyidae (Acari; Trombidiformes) in the shoots was significantly lower in the compost treatment in 2022 (20% of the shoots were occupied/damaged) compared to the mineral treatment (60% of the shoots were occupied/damaged). Araneae abundance was significantly higher (p = 0.033) in the compost treatment compared to the mineral treatment. However, under traditional management, no clear effect on arthropod assemblage was observed. In conclusion, the addition of compost to the superintensive grove helped to limit the presence of some arthropod pests compared to mineral treatment, contributing to a more sustainable crop. Grove type management appeared to play a significant role in the arthropod assemblages and effect of compost addition, but future research utilizing a greater number of groves (replicates) and an extended observation period should be performed to confirm these results.