The Rio San Juan metamorphic complex (RSJC) exposes a segment of a high-P accretionary prism, built during Late Cretaceous subduction below the intra-oceanic Caribbean island-arc. In this paper we present new detailed maps, tectonostratigraphy, large-scale structure, mineral chemistry, in situ trace element composition of clinopyroxene (Cpx), and bulk rock geochemical data for representative garnet-free peridotites and mafic metaigneous rocks of the Cuaba and Helechal tectonometamorphic units of the southern RSJC. The Cuaba subcomplex is composed of upper foliated amphibolites and lower garnet amphibolites, retrograded (coronitic) eclogites, and heterogeneous metagabbros metamorphosed to upper amphibolite and eclogite-facies conditions. The lenticular bodies of associated peridotites are Cpx-poor harzburgites. The underlying Helechal subcomplex is composed of Cpx-poor harzburgites, Cpx-rich harzbugites, lherzolites and rare dunites.The presented data allow us to argue that the Cuaba subcomplex: (a) represents tectonically deformed and metamorphosed crust of the Caribbean island-arc, (b) contains fragments of its supra-subduction zone mantle, and (c) includes different geochemical groups of mafic protoliths generated by varying melting degrees of diverse mantle sources. These geochemical groups include mid-Ti tholeiites (N-MORB), normal IAT and calc-alkaline rocks, low-Ti IAT, metacumulates of boninitic affinity, and HREE-depleted IAT, that collectively record a multi-stage magmatic evolution for the Caribbean island-arc, prior to the Late Cretaceous high-P metamorphism. Further, these mafic protoliths present comparable geochemical features to mafic igneous rocks of the Puerca Gorda Schists, Cacheal and Puerto Plata complexes, all of them related to the Caribbean island-arc. These relations suggest that the southern RSJC complex represents part of the subducted fore-arc of the Caribbean island-arc, which experienced initial subduction, underplating below the arc, and final exhumation in the Caribbean subduction-accretionary prism. The absence of a thick section of mafic–ultramafic cumulates also suggests delamination and/or thermomechanical erosion at the base of the Caribbean arc section during an advanced arc stage.