Zingiber officinale Roscoe rhizomes have been associated with multiple health benefits, such as blocking blood clotting, digestive and antinausea effects and aid in respiratory conditions. These effects have been linked with their polyphenolic main metabolites, gingerols and shogaols. Herewith, we report a detailed study on the polyphenolic profile and in the contents of main gingerols and shogaol as well as the antioxidant activity of extracts from Z. officinale rhizomes (n = 17) produced in Costa Rica. Using UPLC-QTOF-ESI MS, a total of 34 polyphenols were identified, grouped in 12 types of structures. In addition, our findings on the main metabolites using UPLC-DAD show all rhizomes complying with total gingerols (TG) content established by the United States Pharmacopeia (USP). At an individual level, samples SR-1 and NR-4 show the higher contents and also exhibit the highest Folin–Ciocalteu (FC) reducing capacity results as well as the best DPPH antioxidant values. In addition, Pearson correlation analysis results showed positive correlation (p < 0.05) between TG and 6-gingerol with FC results and negative correlation (p < 0.05) between 6-gingerol, TG and FC with DPPH results. In turn, Principal Component Analysis (PCA) indicated variability in the composition associated with their region of origin and confirmed that NR-3, NR-4, and especially SR-1 stand out significatively, showing the highest PC1 because of its particularly high TG, 6-gingerol and antioxidant activities. Finally, results from controlled experimental plots of Z. officinale rhizomes (n = 6) indicated influence on metabolites content with higher values for a shorter harvest time and high tunnel cultivation. Therefore, our findings indicate the value of Z. officinale in the elaboration of products with potential benefits for health, delivering extracts with higher levels of gingerols than previous reports and exhibiting high antioxidant activity.