Stable emissive carbon nanodots were generated in zeolite crystals using near infrared photon irradiation gradually converting the occluded organic template, originally used to synthesize the zeolite crystals, into discrete luminescent species consisting of nano-sized carbogenic fluorophores, as ascertained using Raman microscopy, and steady-state and time-resolved spectroscopic techniques. Photoactivation in a confocal laser fluorescence microscope allows 3D resolved writing of luminescent carbon nanodot patterns inside zeolites providing a cost-effective and non-toxic alternative to previously reported metal-based nanoclusters confined in zeolites, and opens up opportunities in bio-labelling and sensing applications.