The adaptation of autochthonous olive varieties to local soil and climatic conditions can lead to a unique chemical composition and characteristics of olive oils that may differ from the generally accepted quality standards set out in the International Olive Oil Council strategy documents and EU regulations. Therefore, the fatty acid composition, biophenol, tocopherol, sterol and triterpenic dialcohol content and composition of the autochthonous Slovenian olive varieties 'Buga', 'Črnica' and 'Drobnica' were studied for a three-year period with the aim of valorising the characteristics of the three olive varieties. Standardised and accredited analytical methods in accordance with SIST EN ISO/IEC 17025:2017 were applied. The results of the investigation showed that the highest average amount of oleic acid (75.75%) was found in the oils of the 'Črnica' variety, followed by the 'Drobnica' (72.06%) and the 'Buga' (68.73%). All three varieties are a good source of total biophenols ('Buga' 616 mg/kg, 'Drobnica' 569 mg/kg and 'Črnica' 427 mg/kg) and α-tocopherol ('Buga' 378 mg/kg, 'Drobnica' 279 mg/kg, and 'Črnica' 243 mg/kg). 'Buga' and 'Drobnica' are characterised by high amounts of total sterols, 2468 mg/kg and 2391 mg/kg, respectively, while 'Črnica' oils, in comparison, showed a lower average value of total sterols (1351 mg/kg). Due to their exceptional chemical composition, 'Buga', 'Črnica' and 'Drobnica' show great potential for the further cultivation and valorisation of traditional olive oil production in the region, thus contributing to the preservation of biodiversity and local traditions. The quality parameters of olive oil from the autochthonous Slovenian olive varieties 'Buga', 'Črnica' and 'Drobnica' also fulfil the limits for extra virgin olive oil according to the Commission Delegated Regulation (EU) 2022/2104, despite local climatic influences. However, accelerated growth due to climatic changes affecting early harvest can lead to them falling outside these limits, which was observed in particular for the 'Buga' variety in terms of the linoleic acid content. This study emphasises the importance of timing the harvest to achieve optimum maturity and meet EU quality standards, taking into account the genetic makeup of the varieties and their response to the current climatic conditions.