The behavior of mono-disperse colloidal particles in a chromonic liquid crystal was investigated. Poly(methyl methacrylate) spherical particles with three different functionalizations, with and without surface charges, were utilized in the nematic and columnar phases of disodium cromoglycate solutions. The nematic phase was completely aligned parallel to the glass substrates by a simple rubbing technique, and the columnar phase showed regions of similar alignment. The behavior of the colloidal particles in the chromonic liquid crystal depended critically on the functionality, with bromine functionalized particles not dispersing at all, and cationic trimethylammonium and epoxy functionalized particles dispersing well in the isotropic phase of the liquid crystal. At the transition to the nematic and especially the columnar phase, the colloidal particles were expelled into the remaining isotropic phase. Since the columnar phase grew in parallel ribbons, the colloidal particles ended up in chain-like assemblies. Such behavior opens the possibility of producing patterned assemblies of colloidal particles by taking advantage of the self-organized structure of chromonic liquid crystals.