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Amid the dual challenge of adapting to and mitigating climate change, greenhouse production is expanding. Greenhouse systems present promising avenues for sustainable intensification, yet their sustainability remains constrained by fertilization practices. Plant-based fertilizers like alfalfa meal represent a promising alternative to contentious organic fertilizers, but their ability to sustain productivity in highly intensive systems is uncertain. This study aimed to (i) compare ecosystem service provisioning between soil-based and soilless greenhouse systems and (ii) evaluate the potential of substituting a standard organic fertilization regime with alfalfa meal. In total, 11 indicators of ecosystem (dis)services associated with food production, climate/soil regulation, and air/water pollution were assessed over two crop cycles, grown under three fertilization regimes, where 0%, 50%, or 100% of N was supplied as alfalfa meal, alongside a control. The soilless system reduced disservices linked to N losses (N2O, NH3, and N leaching) but increased CH₄ emissions. Across systems, alfalfa meal decreased N losses while enhancing soil N and C pools, earthworm, bacterial, and fungal abundance. In the soil-based system, yields were largely unaffected by N substitution, reflecting strong reliance on soil N reserves, as indicated by the low fertilizer recovery (28.3%). In the soilless system, partial N substitution with alfalfa meal maintained yield, even though fertilizer recovery was high (75.3%). This work provides the first comparative study of soil-based and soilless greenhouse systems and the first report on alfalfa meal use in intensive greenhouse production. Total N losses were low (1.1–4.0% of applied N), well below values reported in previous studies, confirming that both cultivation methods can sustain high provisioning services while limiting disservices linked to N losses. Our findings also demonstrate that alfalfa meal is an effective N source, and future research should focus on refining its integration through whole-system approaches that balance trade-offs between ecosystem services.