Abstract The Philippines preserves evidence of the superimposition of tectonic processes in ancient and present‐day collision and subduction zone complexes. The Baguio District in northern Luzon, the Palawan–Central Philippine region and the Mati–Pujada area in southeastern Mindanao resulted from events related to subduction polarity reversal leading to trench initiation, continent‐arc collision and autochthonous oceanic lithosphere emplacement, respectively. Geological data on the Baguio District in Northern Luzon reveal an Early Miocene trench initiation for the east‐dipping Manila Trench. This followed the Late Oligocene cessation of subduction along the west‐dipping proto‐East Luzon Trough. The Manila Trench initiation, which is modeled as a consequence of the counter‐clockwise rotation of Luzon, is attributed to the collision of the Palawan microcontinental block with the Philippine Mobile Belt. In the course of rotation, Luzon onramped the South China Sea crust, effectively converting the shear zone that bounded them into a subduction zone. Several collision‐related accretionary complexes (e.g. Romblon, Mindoro) are present in the Palawan–Central Philippine region. The easternmost collision zone boundary is located east of the Romblon group of islands. The Early Miocene southwestward shift of the collision boundary from Romblon to Mindoro started to end by the Pliocene. Continuous interaction between the Palawan microcontinental block and the Philippine Mobile Belt is presently taken up again along the collisional boundary east of the Romblon group of islands. The Mati–Pujada Peninsula area, on the other hand, is underlain by the Upper Cretaceous Pujada Ophiolite. This supra‐subduction zone ophiolite is capped by chert and pelagic limestones which suggests its derivation from a relatively deep marginal basin. The Pujada Ophiolite could be a part of a proto‐Molucca Sea plate. The re‐interpretation of the geology and tectonic settings of the three areas reaffirm the complex geodynamic evolution of the Philippine archipelago and addresses some of its perceived geological enigmas.