Flow-only and coupled flow-diffusion experiments at 95 °C and 100 bars pCO2 carried out in micro-capillary tubes packed with forsterite mineral grains were used to constrain a coupled classical heterogeneous nucleation and crystal growth reactive transport model describing the formation of secondary magnesite. The study made use of a novel experimental setup in which one capillary tube for flow is connected via a three-way tee to a perpendicular capillary tube sealed at the distal end in which only molecular diffusion is allowed to occur—an experimental analogue of a single fracture-rock matrix system. While the high flux of CO2 bearing fluids and their low pH did not result in the formation of secondary carbonates in the flow-dominated channels, as much as 2.7% magnesite formed in a diffusion-controlled capillary tube sample after 300 hours of reaction. The precipitation of secondary magnesite was not uniformly distributed, however, but showed a distinctive peak shaped pattern along the sample reacted as quantified by RAMAN spectroscopic analysis. About 50% of the total magnesite precipitation formed within a narrow interval of a few millimeters close to the middle of the 3 cm diffusion sample. To simulate the behavior of the diffusion–reaction column, and in particular the pronounced mm scale peak at approximately 1.8 cm, an interfacial free energy of approximately 70 mJ·m−2 combined with a relatively high crystal growth rate for secondary magnesite was required. In agreement with the observations based on RAMAN spectroscopy, the simulations suggest that more than 50% of Mg2+ dissolved from the primary forsterite precipitated as secondary magnesite. The magnesite precipitation at the central peak position in the diffusion sample showed such rapid growth that it created a local minimum in pore fluids Mg2+ concentration close to the peak, creating a “nucleation shadow” that focused continued growth there as nearby regions had no nucleation seeds available for crystal growth. Continued crystal growth on the initial magnesite band acted to further increase the reactive surface area at this point, thus enhancing the spatially focused crystal growth rate and creating a positive feedback leading to pattern formation. This highlights the potentially critical role of an initial nucleation event in controlling mineral precipitation patterns in subsurface porous media, patterns that may determine how the pore structure subsequently evolves physically and chemically over time due to reactive flow and transport.