This study elucidates the effect of colony formation on light absorption by Botryococcus braunii microalgae cells. The spectral average mass absorption cross-section of suspensions of B. braunii cultures with free-floating cells or colonies was measured experimentally across the photosynthetically active radiation region. The average mass absorption cross-section was found to decrease significantly across the spectrum in the presence of colonies. This observation could be attributed to (i) reduced pigment concentrations due to nutrient limitations, (ii) mutual shading of the aggregated cells, and/or (iii) the presence of the colonies' extracellular matrix. The Monte Carlo ray tracing method was used to elucidate the contribution of each of these phenomena on the mass absorption cross-section of cells in colonies. Colonies were modeled either as fractal aggregates of monodisperse cells or as an ensemble of monodisperse cells regularly arranged at the periphery of a hollow sphere embedded in a spherical extracellular matrix or as a volume and average projected area equivalent coated sphere. The change in pigment concentrations due to nutrient limitation was found to be the most important factor. In addition, the mass absorption cross-section of cells in colonies was found to decrease due to mutual shading among cells. This effect was stronger with increasing number of cells in the colony and increasing cell absorption index. The effect of extracellular matrix on the mass absorption cross-section was found to be negligible. Finally, good agreement was found between the equivalent coated sphere approximation and the colonies modeled as fractal aggregates comprised of monodisperse cells. This study also established that the Monte Carlo ray tracing method can be used for a variety of microalgae species and colony configurations, whose absorption cross-section are not readily calculated by standard methods due to their complex geometry, inhomogeneous nature, and large size compared to the wavelength of the incident light.