Mafic-ultramafic intrusions within continental flood basalt terrains are frequently associated with Cu-Ni-PGE mineralization. This study aims to constrain the petrogenesis of early crystal phases in a promising exploration target, the Morungava mafic-ultramafic intrusion that is associated with the Parana flood basalts. Therefore, we analyzed the composition of chromiferous spinel and associated olivine of ultramafic rocks from the sill-like intrusion. Samples were selected from different drill core intervals with high MgO and Cr contents. Two generations of Cr-spinel and olivine were identified in olivine gabbronorite and wehrlite rocks from the intrusion. The first type (Spl1) is enclosed in the core of high-Mg idiomorphic olivine crystals (Ol1) and has higher Cr2O3 (28–35 wt.%), Al2O3 (13–33 wt.%), MgO (12.6–14.6 wt.%), and lower TiO2 (0.5–0.8 wt.%) compared to the second type of spinel (Spl2). Spl2 occurs in the interstitial space between olivine and clinopyroxene and contains higher TiO2 (2.0–15.8 wt.%) and lower Al2O3 (5.2–10.5 wt.%), Cr2O3 (10–25 wt.%), and MgO (2.8–7.6 wt.%) contents. Geothermometric calculations using high-Mg idiomorphic Ol1 - Spl1 pairs resulted in temperatures below the corresponding solidus, indicating subsolidus exchange between these minerals and accounting for the Cr-Al trend in Spl1. The high Mg-contents, normal zoning and high but decreasing Cr contents in Ol1 are consistent with crystallization at an early stage during progressive fractional crystallization. Fractionation of olivine, Cr-spinel, clinopyroxene, and plagioclase deceased Mg, Al, and Cr, and increased Fe and Ti in the residual melt. The compositional hiatus with the low-Mg olivine (Ol2) and especially with Spl2 crystals most likely reflects crystallization from an evolved interstitial liquid at a time where Ol1-Spl1 were relatively isolated from diffusional interaction, in addition to solvus processes in spinel. The Fe-Ti- trend in Spl2 likely reflects varying degrees of evolution of the interstitial melts. The Morungava intrusion thus records a complex history of extensive reactions that started with fractionating Ol1-Spl1 in a magma chamber that experienced periodic magma addition, and finished in trapped, interstitial, in situ intercumulus liquids (Ol2-Spl2). The setting, host rocks, and geochemical characteristics of the Morungava intrusion are reminiscent of the Cu-Ni-PGE mineralized Noril’sk-Talnakh ultramafic complex, confirming the inferred mineralization potential.