We use cross-sectional transmission electron microscopy to study the damage induced below the surface of indium phosphide (InP) samples by single and multiple femtosecond laser pulses with a photon energy lower than the InP band gap. Single-pulse irradiation creates a ∼100 nm deep crater with a resolidified surface layer consisting of quasiamorphous indium phosphide. The resolidified layer has a thickness of ∼60 nm at the center and extends laterally beyond the edge of the crater rim. Exposure to multiple femtosecond pulses of 2050 nm center wavelength results in the formation of laser-induced periodic surface structures (LIPSS) with two different periods, one (∼1730 nm) less than but close to the laser wavelength and one (∼470 nm) four times smaller. Segregation beneath both types of ripples leads to the formation of In-rich particles embedded in the resolidified surface layer. Extended defects are detected only below the center of the multiple-pulse crater and their distribution appears to be correlated with the LIPSS modulation. Finally, LIPSS formation is discussed in terms of the observed subsurface microstructures.