Background Nudging is increasingly used to promote healthy food choices in supermarkets. Ordering groceries online is gaining in popularity and nudging seems efficacious there as well, but is never comprehensively tested in real-life. We evaluated the real-life effectiveness of nudging in an online supermarket on healthy food purchases. Methods We conducted a multi-arm, parallel-group, individually randomized controlled trial in an online supermarket. During 1 month, all customers were randomized to (1) control condition, (2) information nudges, (3) position nudges, and (4) information and position nudges combined. Allocation was concealed and customers were not blinded, but unaware of the intervention. Mean differences between the control condition and the intervention arms in the total percentage of healthy purchases were assessed with a linear mixed model. We tested for effect modification by area-level deprivation. Results Based on sales data from 11,775 shoppers, no overall significant effects were detected. Yet, effects were modified by area-level deprivation (pArm 2 < 0.001). Among shoppers from deprived areas, those allocated to information nudges purchased a 2.4% (95%CI 0.8, 4.0) higher percentage of healthy products compared to controls. No significant differences were observed for position (− 1.3%; 95%CI − 2.8, 0.3) and combined nudges (− 0.1%; 95%CI − 1.7, 1.5). Shoppers from non-deprived areas exposed to information nudges (− 1.6%; 95%CI − 3.2, − 0.1) and the combined nudges (− 2.1%; 95%CI − 3.6, − 0.6), but not position nudges (− 0.9%; 95%CI − 2.4, 0.7), purchased a lower percentage of healthy products. Conclusion Information nudges in an online supermarket can increase healthy product purchases, but only for those living in deprived areas. The adverse effects found on purchasing behaviors for those from non-deprived areas call for further research. Further research should also focus on real-life effects of online healthy food nudging as part of a broader nutrition intervention strategy, and on the equitability of the online nudging intervention within populations. Trial registration Retrospectively registered in the ISRCTN registry at May 21, 2021 (ISRCTN10491616).