We report the design of a setup combining the simultaneous and independent optical trapping and second-harmonic generation (SHG) of 1 µm diameter silica microspheres with two independent laser beams. Optical trapping is achieved with a tightly focused continuous wave infrared laser beam whereas the SHG intensity from the trapped microparticles is obtained with a 810 nm femtosecond pulsed laser. The silica microparticles are dispersed in an aqueous solution, and a microfluidic channel flow is used to remove untrapped microparticles. We show by the perpendicular displacement of the optical trap from the microfluidic channel wall that it is possible to control the contribution of the channel wall/solution interface to the overall SHG intensity. Stable trapping and SHG detection of two microparticles is also demonstrated. Combining the independent trapping of centrosymmetrical silica microparticles with SHG offers new avenues for analytical studies like surface sensing or all-optical devices where the SHG intensity is controlled by the trapping beam.