Apart from being a foremost source of calories for a large part of the world’s population, cultivated rice (Oryza sativa) provides beneficial effects for human health through several bioactive compounds, including phenolics. Therefore, to earn this advantage, it is essential to retain the phenolics through appropriate post-harvest practices. In this paper, the profile of 10 individual phenolic compounds contained by rice grains after drying, dehusking and polishing processes were studied. A number of Indonesian rice cultivars from indica and javanica subspecies were acquired from conventional (IR-64, Umbul-umbul and Pandanwangi) and organic farming (Batang Lembang, Pandanwangi, black- and red-pigmented rice) were studied. Additionally, the effect of polishing degree on individual phenolics content in the grain was also evaluated. The level of phenolics decreased, also their relative values dramatically changed throughout a series of post-harvest processes. Moreover, changes on the composition of phenolic acids and its aldehydes in the grain have been described. p-Coumaric acid reflects the greatest differences on the phenolic composition during the course of post-harvest practices that altered from 48% to 8% portion to the total phenolics in paddies and polished grains, respectively. However, phenolics content in black-pigmented rice appeared to be the most persistent in the rice matrix. Since the profile of individual phenolics has also been evaluated on different polishing degrees (70%, 80%, 90% and 100% bran removal), the distribution of these compounds in the whole grain rice was effectively disclosed. These variations in the compositions and quantities of phenolics revealed the effect of post-harvest practices, varietal differences as their distribution in the grain.