Asphaltene deposition from crude oil, induced by n-heptane and acetone flows in a microfluidic device, was studied by optical and FTIR spectroscopic imaging techniques in situ. It was found that n-heptane and acetone penetrate crude oil in completely different ways, which is responsible for the formation of deposits with different structures and chemical compositions. The contact of the n-heptane flow with crude oil leads to fast aggregation of asphaltenes at the interface, resulting in the formation of a compact deposit fixed to the surface. Subsequent slow diffusion of n-heptane into crude oil causes asphaltene aggregation and precipitation of loose deposits. In the case of acetone, the flocculant diffuses (faster than n-heptane) into crude oil, which results in removal of its soluble components and in the formation of deposits appearing as strips as well. The distribution of the functional groups (–OH(NH), CH2–CH3, C=O, C–O, S=O) in the deposits is spatially heterogeneous. The asphaltenes deposits formed at the flocculant-crude oil interface are richer in the functional groups than those formed during diffusion. No carbonyl groups were revealed in the deposits formed in the acetone flow, while oxygen-containing groups such as –OH(NH) and S=O were present, which was an unusual result.