Insufficiently treated wastes contained within onsite sanitation systems (OSS) commonly used by disadvantaged and developing communities contribute to public and environmental health concerns, calling for practical alternative solutions. At the basic level, an improved understanding of the evolution of chemical and physical constituents under different waste introduction methods and for short-term and long-term operation is needed. While receiving non-dilute waste under mixed, unmixed, toilet paper exclusion, and urine diversion (UD) regimes, self-flushing OSS simulated using anaerobic digesters (ADs) were compared during three operational stages: (1) 0–1 month service for unsheltered encampments; (2) 1–3 month disaster relief scenario; and (3) ≥ 3 months representing refugee camps and long-term household use. Although stratification was found to promote suitable conditions for short-term use of self-flushing toilets, mixing increased beneficial biodegradation of organic constituents. Urine-containing ADs demonstrated a shift from sulfide to ammonia odor accompanied by high pH (> 8) after ~ 240 d.E. colireduction following elevated nitrogen and dissolved solids levels pointed to decreased pathogen survival in ADs with urine. The benefits of bacterial disinfection, reduction of sulfurous odors, and heightened organics degradation in mixed, urine-containing ADs suggest this format as more desirable for prolonged use of self-flushing OSS over unmixed or urine-diverting formats.