Cultivated rice (Oryza sativa) is a global staple food that subsists calories for more than half of the world’s population. Emerging evidence supports that a number of health-promoting substances have been identified in rice including phenolic compounds. Hence, individual profile of these compounds is essential to determine in both raw and processed grains. Pressurised Liquid Extraction (PLE) followed by High Performance Liquid Chromatography coupled with Photo-diode Array detector (HPLC-PDA) has been utilised as reliable analytical techniques for the extraction and quantification. Multivariate analyses based on seventeen phenolic compounds clustered the ten tested rice samples according to their species, pigments and grain productions. The level of these compounds was then individually monitored during the course of rice production of Indonesian rice varieties obtained from conventional (IR-64, umbul-umbul and pandan wangi) and organic farming (batang lembang, pandan wangi, black and red pigmented rice). Phenolics content in black pigmented rice appeared to be the most persistent in the matrix during rice production. However, in general, the level of phenolics decreased throughout a series of rice production with the most influential factors were de-husking and polishing. These particular processing steps led to phenolics losses of up to 86% as well as the changes on the composition of phenolic acids and its aldehydes in the grain. 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 mapped. These variations in the compositions and quantities of phenolics disclosed the effect of processing steps, varietal differences as well as their distribution in the grain. Hence, the results from this study could help rice producers to optimize levels of these compounds in the final rice product by selecting the right varieties and appropriate production processes.