Encapsulation of organic molecules in carbon nanotubes has opened a new route for the fabrication of hybrid nanostructures. Here we show that diameter-selective encapsulation of two metallocene compounds bis(cyclopentadienyl) cobalt and bis(ethylcyclopentadienyl) cobalt has been observed in single-walled carbon nanotubes. In particular, bis(cyclopentadienyl) cobalt is observed to fill only nanotubes of one specific diameter. Electron transfer from the cobalt ions to the nanotubes has been directly observed through a change in the charge state of the encapsulated molecules. The filling of the tubes is found to induce a red-shift of the photoluminescence emission, which is attributed to the formation of localized impurity states below the conduction band of the nanotubes.