The self-rooted plum genotype ‘Mrkosljiva’ was first selected as it was devoid of Sharka leaf symptoms during the 5‑year study (2009–2014), which was subsequently confirmed by negative ELISA test results. Hence, the aim of the study was to investigate the biochemical variability of the autochthonous ‘Mrkosljiva’ plum genotype, based on its sugar, acid and phenolic compounds content during 3 years. In 2010 and 2011, the plums tasted sweet with favourable sugar:acid ratios of 55:1 to 65:1. These plum fruits were collected at the full ripeness stage from an extensive orchard located in northeastern Bosnia and Herzegovina (45 °N). Analysis by HPLC identified the following polyphenolic compounds—chlorogenic acid, cyanidin-3-O-glucoside, cyanidin-3-O-rutinoside, neochlorogenic acid, quercetin-3-O-galactoside and quercetin-3-O-rutinoside—in all 3 years that were evaluated (2009–2011), but in different amounts, depending on the environmental conditions of each year. In 2009, the plums were healthier with a threefold greater phenol content than during the other 2 years of growth. In 2009, protocatechuic acid was detected, whereas catechin, procyanidin B1, procyanidin B2 and quercetin-3‑O-rhamnoside were not detected. The combination of high phenol and sugar content in ‘Mrkosljiva’ provides healthy and tasty plums suitable primarily for processing, and to a lesser extent, due to their size, for fresh fruit marketing.