A nanodiamond‐rich fraction (NDF) separated from the Orgueil meteorite was subjected to a high‐intensity ultrasonic treatment in a weakly acidic aqueous solution. After sedimentation by centrifugation, two fractions of grains (suspension, designated as OD7C and sediment, designated as OD7D) with different properties have been obtained. The following effects of the sonication were revealed from comparison of the contents and isotope compositions of C, N, and Xe released during stepped pyrolysis and combustion of the fractions OD7C and OD7D, the initial NDF and two grain‐size fractions (OD10 and OD15) produced without sonication (a) surface layer of the sonicated diamond grains is modified to different extent in comparison with nontreated ones, (b) in some grains concentrations of the bulk N and Xe a reduced significantly, and (c) nondiamond nitrogen containing phases (e.g., Si3N4) have been destroyed. It is suggested that combined effects of the sonication and centrifugation observed for the fractions OD7C and OD7D are due to differences in surface chemistry of the nanodiamond grains, which statistically influences behavior of nanoparticles during the sonication resulting in their preferential modification in the different reaction zones of the cavitating fluid.