A method is presented which enables analysis of lignin precipitated on the surface of kraft pulp fibers. As experimental input, high-resolution atomic force microscopy phase images of the fiber surfaces have been recorded in tapping mode. A digital image analysis procedure—based on the watershed algorithm—is applied to distinguish between cellulose fibrils and the precipitated lignin. In this way, size distributions for the diameter of lignin precipitates on pulp fiber surfaces can be obtained. In an initial application of the method, three softwood kraft pulps were analyzed: a black liquor cook with a very high content of precipitated lignin, a bleached pulp where nearly no precipitated lignin is visible and an unbleached industrial pulp. The proposed method is suggested as an appropriate tool to investigate the kinetics of lignin precipitation and the structure of lignin precipitates in pulping and bleaching.