Rolling circle amplification (RCA) is a robust isothermal nucleic acid amplification method producing nanocomposites of DNA and inorganic magnesium pyrophosphate precipitates. Although the conformation and structure of such nanocomposites impact applications, most studies of them have been performed at the end‐point after exposure to a treatment. Here, we use real‐time optomagnetic measurements of the hydrodynamic size of magnetic nanoparticles (MNPs) to study the growth of RCA products grafted onto MNPs as well as the effect of post‐RCA temperature annealing and chemical treatment. As a key result, we show that secondary structures in the RCA products trap and partially protect magnesium pyrophosphate precipitates and that these are reversibly released upon heating above a characteristic temperature defined by the sequence of the RCA product. These findings provide a deeper mechanistic understanding of the synthesis and structure of DNA nanocomposites, which impacts applications of DNA nanocomposites in sensing and drug delivery.