The characterization and control of the phase of broadband femtosecond pulses in nonlinear microscopy are successfully demonstrated with a collinear configuration of spectral shear interferometry for direct electric field reconstruction (SPIDER). A femtosecond-pulse shaper is used as a dispersionless interferometer for the measurement of the spectral phase and to actively compress a broadband supercontinuum from a photonic crystal fiber. This allows in situ online phase management and enables the application of quantum control spectroscopy in microenvironments.