Humid-tropical Ultisols supporting smallholder horticulture in Southeast Asia are widely recognised as degraded agroecosystems whose biogeochemical functioning has been disrupted by accelerated cation leaching, sulfur depletion following reduced atmospheric S deposition, and decades of chloride-loaded fertilisation. From an ecological engineering perspective, restoring the productive capacity of these soils requires interventions that simultaneously address nutrient cycling, soil-microbiome connectivity, and avoidance of off-site externalities, rather than yield optimisation alone. This study evaluated potassium sulfate (K₂SO₄) as an ecologically engineered substitute for potassium chloride (KCl) in a degraded humid-tropical Ultisol of Indralaya Selatan, Ogan Ilir, South Sumatra, Indonesia, using shallot (Allium cepa var. aggregatum L.) as a sentinel crop. A Randomised Complete Block Design with four K₂SO₄ doses (0, 60, 90, 120 kg ha⁻¹) and three replications (n = 12) was implemented across an eight-week growing season. Fourteen plant-level state variables describing canopy, photosynthetic and harvest-organ traits were monitored and combined with site-level inputs to estimate avoided chloride load and net sulfate input to the agroecosystem. Multivariate ordination (PCA, 63.1% cumulative variance) positioned the 90 kg ha⁻¹ treatment in the high-functioning quadrant aligned with bulb dry weight, shoot dry weight, bulb volume and chlorophyll, while supraoptimal dosing (120 kg ha⁻¹) shifted system state back toward control, consistent with the self-organising response expected of ecologically engineered nutrient pathways. Pearson connectivity analysis revealed a coherent yield-component cluster (bulb diameter–bulb dry weight, r = .909, p < .01) interpretable as a functional ecological module mediated by K⁺-driven turgor and S-dependent structural integrity. An OLS model (R² = .827) is proposed as a non-destructive ecological monitoring tool for in-field state assessment. Substitution of K₂SO₄ at 90 kg ha⁻¹ for an equivalent K-rate of KCl avoided an estimated ~32 kg Cl⁻ ha⁻¹ season⁻¹ entering the rooting zone and added ~16 kg S ha⁻¹ to the soil S pool, quantifying a tangible nature-based-solution benefit. The findings advance an ecologically engineered nutrient-pathway framework chloride-free, dual K–S supply, dose-bounded by ecosystem self-organisation, and coupled to non-destructive monitoring for the restoration of productive function in degraded humid-tropical Ultisol agroecosystems.