Cretaceous plutons of the Peninsular Ranges batholith (PRB) intruded two different host rock sequences in the central part of the Baja California peninsula, Mexico. The western sequence is the volcanic-volcaniclastic Alisitos oceanic arc, and the eastern lithologies are mainly metasedimentary pre-Mesozoic units. We analyze the ~116 Ma San Jerónimo (SJe) pluton in the PRB western zone and the Compostela (COM) and San Pedro (SP) plutons (~97 Ma and ~104 Ma, respectively) in the PRB eastern zone. The SJe pluton varies from pyroxene-hornblende gabbro to hornblende-biotite tonalite. Their rocks are subalkaline, calcic/calc-alkaline, and metaluminous, which are akin to island arc granite settings; and yield εNdt values of +5.6 and +6.8, indicating a depleted mantle source without discernible crustal assimilation. The SJe pluton shows subparallel REE patterns (LaN/YbN = 0.5–4.4), with progressive enrichments in REE abundances in the tonalites, suggesting differentiation by fractional crystallization of a single magmatic system. Also, show low Sr/Y values (t values from +4.2 to −2.3, indicating mantle-derived melts with the contribution of assimilated crustal material. Their strongly fractionated REE patterns (LaN/YbN = 8–38.3) are characteristic of evolved melts or magmas differentiated within the crust. The high Sr/Y (~90) and La/Yb (~21) further suggest thicker crustal zones (>45 km). Permeation features and parallelism between the metamorphic foliations of the prebatholithic rocks and the magmatic foliation of the plutons indicate a post-deformational emplacement of the mid-Late Cretaceous plutons of the southern PRB. Our data restricts the deformation event before ca. 100–105 Ma.