A multi-analytical strategy for the valorisation of goldenberry calyx, a promising source of health-promoting compounds, is presented in this work. A comprehensive characterization of P. peruviana calyx extracts, obtained by an optimized pressurized liquid extraction (PLE) procedure, is developed applying first an ultra-high-performance liquid chromatography coupled to quadrupole time-of-flight tandem mass spectrometry (UPLC-ESI-q-TOF-MS/MS) method in positive and negative electrospray ionization (ESI) mode. A total of fifty-six phytochemicals, including major phenolic components, several withanolides (C28-isoprenoids) with a variety of biological activities, and a large family of anti-inflammatory sucrose esters were tentatively identified using this methodology. An integrated identification strategy based on accurate mass data obtained by high resolution mass spectrometry (HRMS), ion source fragmentation, MS/MS fragmentation patterns, generated molecular formulae and subsequent unsaturation degree calculation, along with database and bibliographic search is proposed. Isobaric withanolides-type compounds were tentatively identified or classified according to their different hydroxy and epoxy positions, on the basis of the complementary information provided by MS/MS product ion spectra obtained in both ESI+ and ESI- mode. The proposed structural elucidation approach provides a valuable contribution to the limited information available regarding the MS/MS structural analysis of withanolides in ESI(-) mode. Moreover, an alternative elucidation strategy based on deconvolution and database search was successfully applied for the phytochemical profiling analysis of the volatile fraction of P. peruviana calyx extracts by gas chromatography quadrupole time-of-flight mass spectrometry (GC-q-TOF-MS), which reveals the presence of relevant terpenoids, including phytosterols and tocopherols (Vitamin E). The results of the phytochemical characterization obtained herein demonstrates the great potential of applying integrated identification strategies to HRMS data obtained from complementary LC- and GC-q-TOF-MS(/MS) platforms, as powerful identification tools for improving our understanding on the phytochemical composition of natural extracts intended to be used in functional foods or in traditional medicine preparations.