Emerging and changing evidence made it necessary to update STOPP-START criteria, and version 2 was published recently. In this study the objectives were to determine the prevalence of potentially inappropriate medication prescribing (PIM) in primary care using STOPP versions 1 (v1) and 2 (v2), as well as 2012 AGS Beers criteria, and analyze the factors associated with inappropriate prescribing according to STOPP/START v2. A cross-sectional study was carried out including community-dwelling older adults over the age of 65. Sociodemographic, clinical, functional and comprehensive drug therapy data were collected. The primary endpoint was the percentage of patients receiving at least one PIM. This variable was measured using three tools: STOPP v1, 2012 AGS Beers criteria and STOPP v2. Similarly, the percentage of patients receiving at least one potential prescribing omission (PPO) was calculated using START versions 1 and 2. A total of 1,615 prescriptions were reviewed. The median number of medications per patient was 7.1 drugs (±3.8). The prevalence of elderly people exposed to polypharmacy (≥5 medications) was 72.9%, whereas 28.4% of the participants took ≥10 drugs regularly. PIM were present in 18.7%, 37.3% and 40.4% of participants, according to the STOPP v1, 2012 Beers criteria and STOPP v2, respectively. According to STOPP v2, the number of medications taken (OR: 1.14, 1.06–1.25), the presence of a psychological disorder (OR: 2.22, 1.13–4.37) and insomnia (OR: 3.35, 1.80–6.32) were risk factors for taking a PIM. The prevalence of PPOs was 34.7% and 21.8% according to version 1 and 2, respectively. In conclusion, STOPP-START criteria have been remarkably modified, which is evidenced by the different prevalence rates detected using version 2, as compared to version 1. In fact, the level of agreement between version 1 and the updated version is only moderate. Special attention should be paid on benzodiazepines, which keep being the most frequent PIM.