Sinus augmentation has become a more predictable and successful procedure as the knowledge of its indications and complications increased. However, knowledge of risk factors leading to early implant failure (EIF) among challenging systemic and local conditions is insufficient. The present study aims to assess risk factors for EIF following sinus augmentation in a challenging cohort. A retrospective cohort study conducted during a period of 8 years in a tertiary referral centre providing surgical and dental health care. Implant and patient variables including age, ASA (American Society of Anesthesiology) physical status classification, smoking, residual alveolar bone, type of anaesthesia and EIF were collected. Cohort was comprised of 751 implants placed in 271 individuals. EIF rates at the implant and patient level were 6.3% and 12.5%, respectively. EIF was found to be higher among smokers (patient level: χ2 (1) = 8.74, p = .003), ASA 2 physical classification patients (patient level: χ2 (2) = 6.75, p = .03), sinuses augmented under general anaesthesia (patient level: χ2 (1)=8.97, p = .003), higher bone gain (implant level: W = 12 350, p = .004), lower residual alveolar bone height (implant level: W = 13 837, p = .001) and multiple implantations (patient level: W = 3016.5, p = 0.01). However, other variables such as age, gender, collagen membrane and implant's dimensions did not reach significance. Within the limits of the study, we can conclude that smoking, ASA 2 physical status classification, general anaesthesia, low residual alveolar bone height and numerous implants are risk factors for EIF following sinus augmentation in challenging cohorts.