Gastroesophageal reflux disease (GERD) is associated with significant morbidity in patients with systemic sclerosis (SSc). Although the introduction of proton pump inhibitors (PPIs) into clinical care have represented a major achievement in the management of oesophago-gastric problems in SSc, PPIs are seldom fully effective in SSc patients, and the utilization of maximum PPI dosages is a very frequent clinical practice. However, currently there is little evidence currently to support the empiric use of PPIs in SSc which is especially relevant in regard to safety concerns of long-term exposure with have been raised in the general population. The purpose of this viewpoint is to highlight the significant beneficial impact of PPIs on GERD in SSc, while considering the potential adverse effects in this patient population. Furthermore, we highlight the unmet needs of SSc patients with GERD, and also propose an agenda for future research to optimise the safe and effective use of PPIs in SSc.