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Pd(II)-compounds are presently regarded as promising anticancer drugs, as an alternative to Pt(II)-based drugs (e.g., cisplatin), which typically trigger severe side-effects and acquired resistance. Dinuclear Pd(II) complexes with biogenic polyamines such as spermine (Pd2Spm) have exhibited particularly beneficial cytotoxic properties, hence unveiling the importance of understanding their impact on organism metabolism. The present study reports the first nuclear magnetic resonance (NMR)-based metabolomics study to assess the in vivo impact of Pd2Spm on the metabolism of healthy mice, to identify metabolic markers with possible relation to biotoxicity/side-effects and their dynamics. The changes in the metabolic profiles of both aqueous and lipophilic extracts of mice kidney, liver, and breast tissues were evaluated, as a function of drug-exposure time, using cisplatin as a reference drug. A putative interpretation was advanced for the metabolic deviations specifically triggered by Pd2Spm, this compound generally inducing faster metabolic response and recovery to control levels for all organs tested, compared to cisplatin (except for kidney lipid metabolism). These results constitute encouraging preliminary metabolic data suggestive of potential lower negative effects of Pd2Spm administration. This research was developed within the scope of the CICECO—Aveiro Institute of Materials, with references UIDB/50011/2020 and UIDP/50011/2020, financed by national funds through the Portuguese Foundation for Science and Technology (FCT/MEC) and when appropriate co-financed by European Regional Development Fund (FEDER) under the PT2020 Partnership Agreement. This work was also funded by the FCT through UIDB/00070/2020 (ALMBC and MPMM), PO-CI-01-0145-FEDER-0016786, and Centro-01-0145-FEDER-029956 (co-financed by COMPETE 2020, Portugal 2020 and European Community through FEDER). It also received financial support from PT national funds (FCT/MCTES, Fundação para a Ciência e Tecnologia and Ministério da Ciência, Tecnologia e Ensino Superior) through the project UIDB/50006/2020. We also acknowledge the Portuguese National NMR Network (PTNMR), supported by FCT funds as the NMR spectrometer used is part of PTNMR and partially supported by Infrastructure Project Nº 022161 (co-financed by FEDER through COMPETE 2020, POCI and PORL, and the FCT through PIDDAC). M.V. thanks the FCT and the PhD Program in the department of Medicines and Pharmaceutical Innovation (i3DU) for their PhD grant PD/BD/135460/2017 and T.J.C. thanks FCT for their PhD grant SFRH/BD/145920/2019, both grants were funded by the European Social Fund of the European Union and national funds FCT/MCTES. published