We introduce a novel methodological framework for robust trend analysis (RTA) using remote sensing data to enhance the accuracy and reliability of detecting significant environmental trends. Our approach sequentially integrates the Theil–Sen (TS) slope estimator, the Contextual Mann–Kendall (CMK) test, and the false discovery rate (FDR) control. This comprehensive method addresses common challenges in trend analysis, such as handling small, noisy datasets with outliers and issues related to spatial autocorrelation, cross-correlation, and multiple testing. We applied this RTA workflow to study tree cover trends in Los Alcornocales Natural Park (Southern Spain), Europe’s largest cork oak forest, analysing interannual changes in tree cover from 2000 to 2022 using Terra MODIS MOD44B data. Our results reveal that the TS estimator provides a robust measure of trend direction and magnitude, but its effectiveness is dramatically enhanced when combined with the CMK test. This combination highlights significant trends and effectively corrects for spatial autocorrelation and cross-correlation, ensuring that genuine environmental signals are distinguished from statistical noise. Unlike previous workflows, our approach incorporates the FDR control, which successfully filtered out 29.6% of false discoveries in the case study, resulting in a more stringent assessment of true environmental trends captured by multi-temporal remotely sensed data. In the case study, we found that approximately one-third of the area exhibits significant and statistically robust declines in tree cover, with these declines being geographically clustered. Importantly, these trends correspond with relevant changes in tree cover, emphasising the ability of RTA to detect relevant environmental changes. Overall, our findings underscore the crucial importance of combining these methods, as their synergy is essential for accurately identifying and confirming robust environmental trends.