Nucleation and growth is a technique widely used to prepare colloids, in which droplets are adsorbed onto substrate particles. Changing the contact angle of the substrates can greatly alter the morphology of the product particles. Here, we investigate the nucleation and growth of 3-methacryloxypropyltrimethoxysilane (MPTMS) both onto Stöber spheres and onto (cross-linked) MPTMS* spheres. The former results in ‘snowman’ particles with a cap-shaped MPTMS* compartment, and we show that their morphology is highly controllable via the MPTMS content in the reaction mixture. The contact angle of the MPTMS* compartment decreases with droplet diameter, suggesting that this wetting process is affected not only by surface tension but also by line tension. In contrast to Stöber spheres, MPTMS* substrate particles yield highly reproducible and tuneable ‘engulfed-sphere’ colloids with an internal reference axis (but a homogeneous mass distribution). These engulfed-sphere particles can be fully index-matched for confocal microscopy on account of their homogeneous refractive index. Suitable index-matching mixtures of polar and of low-polar media are presented, where cyclohexyl iodide (CHI) is introduced as a new medium for colloids of high refractive index. Finally, the index-matched engulfed-sphere colloids are self-assembled into (close-packed and long-range) plastic phases, and the particles’ rotational diffusion inside the crystal phases is tracked via confocal microscopy.