Background: Partial nephrectomy (PN) is the preferred treatment for small, localized kidney tumors. Incomplete resection resulting in positive surgical margins (PSM) can occur after PN. The impact of PSM on the risk of recurrence and survival outcomes is not fully understood. We aimed to explore the relationship between PSM, the risk of recurrence and impact on survival after PN in a large multicenter cohort from Denmark. Methods: This was a retrospective cohort study including patients who underwent PN for renal cell carcinoma (RCC) at three departments in Denmark between 2010 and 2016. Data including pathological features, surgical techniques, and patient follow-up was retrieved from electronic medical health records and national databases. We used a combination of descriptive statistics, comparative analysis (comparisons were carried out by Mann–Whitney Test, independent Student’s t-test, or Pearson’s chi-Square Test), univariate and multivariate logistic regression analyses, and survival analysis methods. Results: A total of 523 patients were included, of which 48 (9.1%) had a PSM. Recurrence was observed in 55 patients (10.5%). Median follow-up time was 75 months. We found a lower incidence of PSM with robot-assisted PN (p = 0.01) compared to open or laparoscopic PN. PSM was associated with a higher risk of recurrence compared to negative margins in univariate analysis, but not multivariate analysis. However, the study was underpowered to describe this association with other risk factors. Overall survival did not differ between patients with PSM and negative margins. Conclusions: Our study presents further evidence on the negative impact of PSM on recurrence after PN for RCC, highlighting the importance of achieving NSM, thus potentially improving clinical outcomes. A surgical approach was found to be the only predictive factor influencing the risk of PSMs, with a reduced risk observed with robot-assisted laparoscopy.