The size of the casein micelles (CM) and the milk fat globules (MFG) vary depending on farming factors, such as seasonal variation and stage of lactation, and cow genetics. The MFG and CM size of milk can influence the renneting behavior and texture of manufactured dairy products. In this work, we investigated the combined effects of MFG and CM size on the onset of gelation, the maximum rate of gelation, the value for G′60 min (the final storage modulus) and G″60 min (the final loss modulus), and tan δ upon renneting. Fractionation of MFG on the basis of size was carried out using laboratory-based centrifugation, whereas milk of predominantly large (184–218 nm) or small (147–159 nm) CM was selected naturally on-farm. Casein micelle size had the dominant effect on curd firmness and gelation rates of milk, where small CM milk formed rennet gels earlier and resulted in a firmer gel than milk with large CM. However, MFG size also influenced the renneting properties. The strongest rennet gels were obtained when large MFG (3.88–5.78 μm) was combined with small CM (153–159 nm). Selecting milk on the basis of the microstructure of key milk components could be achieved by natural selection of dairy cows or via fractionation technologies. Selection may provide a useful tool for efficient manufacturing of different dairy products based on the desirable characteristics specific to each.