Background: Longitudinal evidence about risk and protective factors for suicidal ideation among university students is limited. Methods: 12-month first-onset and persistence of suicidal ideation (SI) among Spanish first-year university students were estimated using baseline (T1) and 12-month follow-up (T2) online surveys. Information about STBs, childhood/adolescence adversities, positive relationships, mental disorders, recent stressful experiences, and university sense of membership was assessed. Logistic regression analysis was used to study risk/protective factors of first-onset and persistence of suicidal ideation (SI). Results: A total of 1,248 respondents (58.9% response) were included. Mean age at baseline was 18.7 (SD = 1.3) and 56.0% were female. 7.3% reported 12-month SI at T2. Incidence of new SI cases was 3.4% and, among students with SI at T1, 21.2% also reported SI at T2 (persistence). Risk factors of T2 SI included 12-month mood disorder at T2 both without (aOR = 12.08 95% CI 5.45-26.80) or with (aOR = 7.2 95% CI 2.91-17.80) lifetime mood at T1, past lifetime suicide attempt (aOR = 8.79 95% CI 2.37-32.64) and plan without attempt (aOR = 4.72 95% CI 2.32-9.61), and 12-month physical or sexual assault (aOR = 3.28 95% CI 1.13-9.46). Twelve-month mood at T2 withoutT1 lifetime mood (aOR = 11.27 95% CI 3.02-42.14) and childhood/adolescence emotional abuse or neglect (aOR = 3.41 95% CI 1.10-10.57) or having been bullied (aOR = 3.2 95% CI 1.08-9.53) were associated with first-onset of SI. Twelve-month mood at T2 either without (aOR = 13.92 95% CI 3.76-51.59) or with (aOR = 8.03 95% CI 2.13-30.29) were associated to T2 SI persistence. University sense of membership was protective for overall 12-month SI at T2 (aOR = 0.25 95% CI 0.12-0.53 for middle tertile), first-onset SI (aOR = 0.1 95% 0.02-0.55 for middle tertile) and persistence (aOR = 0.3 95% CI 0.11-0.81 for middle tertile). Limitations: Analysis was based on self-report data focusing on SI only, and conclusions about the direction of the associations are limited. Conclusions: High proportion of SI suggests the need of suicide prevention strategies. The potential role of university sense of membership in reducing suicidal behaviour among university students deserves further investigation