The sizes of carbon nanoparticles covalently functionalized with streptococcal protein G and streptavidin are investigated. Such nanoparticles are used to develop point-of-care tests. Atomic force microscopy (AFM) and dynamic light scattering (DLS) are used to measure the particle sizes. The average size of the carbon nanoparticles conjugate with protein G was 98 nm (min = 56 nm, max = 142 nm) according to the AFM data and 139 nm according to DLS. The sizes of four carbon-streptavidin conjugates with a storage period from 1 to 22 years are compared by DLS. DLS results have revealed that the partial aggregation of the particles (increasing the average size by 10–20%) probably occurs during the first 3 years of conjugate storage. The further storage of the functionalized nanoparticles does not lead to any alteration in the particle size. Additionally, the regularities of the changes in the particle sizes at the different functionalization steps are studied.