The mechanisms and time scales of magmatism and deformation during orogenesis are important for developing models of lithospheric growth. We summarize the first detailed study of a well-preserved Mesoarchean crustal section from the oldest portion of the Kaapvaal craton, southern Africa, which records the complex interactions between deformation and magmatism during craton assembly ca. 3.3–3.2 Ga. We use chemical abrasion–isotope dilution–thermal ionization mass spectrometry (CA-ID-TIMS) U-Pb zircon geochronology and apatite thermochronology in conjunction with geological mapping to show that the tonalitic to granitic Usutu magmatic suite intruded into the ca. 3.66–3.45 Ga Ancient gneiss complex over a period of ∼16 Ma ca. 3236–3220 Ma as discrete pulses of magma with variable intrusive styles. Usutu rocks retain magmatic fabrics that preserve a history of NW-SE regional shortening, consistent with synchronous deformation recorded in the adjacent Barberton greenstone belt. U-Pb zircon dates of ca. 3.28–3.23 Ga and apatite cooling dates from the Nhlangano gneiss SE of the Ancient gneiss complex reveal that they represent an older, largely undocumented period of crustal growth and modification. Synchronicity in magmatism and similarity in kinematics of deformation north and south of a previously suggested continental suture in the Barberton greenstone belt lead us to propose doubly vergent subduction zones that were active from at least ca. 3.28 to 3.22 Ga. Geochemistry of the Usutu suite reveals differences in magma sources from north to south, which, when combined with Nd isotopic signatures, are consistent with their production in a subduction zone. The combination of <1 Ma precision on crystallization dates with field observations and geochemistry allows us to track the evolution of this magmatic system with temporal resolution unprecedented for Archean rocks.