The late Neoproterozoic São Rafael pluton, located in the Seridó Belt of the Borborema geologic province, northeastern Brazil, is an unfoliated, metaluminous, epidote-bearing, high-K calc-alkalic granitoid. Three facies are present in its northern lobe: (i) a dominant massive granite to quartz monzonite porphyritic facies containing microcline phenocrysts, (ii) subordinate fine-grained facies, similar to the porphyritic facies except lacking amphibole, that crop out as inselbergs (“Serras”), and (iii) rare pillows of microgranular mafic enclaves (MMEs) that are present within the porphyritic facies.Chemical analyses include 19 bulk-rock data, and 33 microprobe data of epidote and amphibole. Beginning with bulk chemistry and postulated mineral compositions, an iterative procedure of solving matrices characterizes a rock sample. Derived information includes: (i) identifying what minerals are present, (ii) their relative abundances, and (iii) their chemical compositions, even for minerals (such as biotite or amphibole) with complexly variable compositions. Calculated mineral compositions are compatible with microprobe data. The matrix solutions further indicate alternative mineral assemblages, and the compositions of “phantom” minerals that could have existed in the magma source, although absent in the pluton. They establish that olivine, but not clinopyroxene, was a possible phantom mineral and that MMEs are of unrelated magmatic origin.According to matrix analysis, amphibole in an outer zone of the porphyritic facies is solely of neoformed origin, whereas amphibole in an inner zone of the porphyritic facies is of mixed origin—partly neoformed and partly residual (i.e., xenocrystic) “patchy” amphibole derived from MMEs. A qualified geothermometer provides Tsolidus = 730 ± 6 °C for the outer subfacies, and a qualified geobarometer provides P = 0.78 ± 0.06 kbar. Amphibole in MMEs crystallized at depth, at P~3.3 kbar. Corroded epidote attests to the pressure-sensitive instability of that mineral during rapid ascent decompression.Cathodoluminescence reveals complexly structured zircons with magmatic overgrowths and inherited cores. 207Pb/206Pb ages of inherited components cluster at ~2.0 Ga and ~2.4 Ga, these ages being prominent in the local basement. Oscillatory-zoned magmatic components yield a concordia upper intercept age of 580 ± 9 Ma, interpreted as the age of igneous crystallization. Values of δ18O in zircon are only slightly higher than δ18O in mantle-like zircon. At 0.58 Ga, εHf in magmatic zircon was notably unradiogenic (−22 to −26), indicating a magma source in old continental crust as adduced by ages of inherited zircon. A U-Pb titanite date is around 0.55 Ga.For the Rb-Sr and Sm-Nd whole-rock systems, isotopic inheritance from the magma protolith is so extreme and variable that isochrons are actually “scatterchrons” that provide no useable age information. Rb-Sr cooling ages of biotite are 498 ± 1 Ma. Most Sm-Nd depleted mantle ages lie in the range of 2.6 ± 0.13 Ga. São Rafael magma was “unregenerate,” not isotopically homogenized when emplaced.