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Nucleosynthetic isotope variability amongst Solar System objects is commonly used to probe the genetic relationship between meteorite groups and rocky planets, which, in turn, may provide insights into the building blocks of the Earth-Moon system1–5. Using this approach, it is inferred that no primitive meteorite matches the terrestrial composition such that the nature of the disk material that accreted to form the Earth and Moon is unconstrained6. This conclusion, however, is based on the assumption that the observed nucleosynthetic variability amongst inner Solar System objects predominantly reflects spatial heterogeneity. Here, we use the isotopic composition of the refractory element calcium to show that the inner Solar System’s nucleosynthetic variability in the mass-independent 48Ca/44Ca ratio (μ48Ca) primarily represents a rapid change in the μ48Ca composition of disk solids associated with early mass accretion to the proto-Sun. In detail, the μ48Ca values of samples originating from the ureilite and angrite parent bodies as well as Vesta, Mars and Earth are positively correlated to the masses of the inferred parent asteroids and planets – a proxy of their accretion timescales – implying a secular evolution of the bulk μ48Ca disk composition in the terrestrial planet-forming region. Individual chondrules from ordinary chondrites formed within 1 Myr of proto-Sun collapse7 record the full range of inner Solar System μ48Ca compositions, indicating a rapid change in the composition of the disk material. We infer that this secular evolution reflects admixing of pristine outer Solar System material to the thermally-processed inner protoplanetary disk associated with the accretion of mass to the proto-Sun. The indistinguishable μ48Ca composition of the Earth (0.2±3.9 ppm) and Moon (3.7±1.9 ppm) reported here is a prediction of our model if the Moon-forming impact involved protoplanets or precursors that completed their accretion near the end of the disk lifetime.