Salt stress severely constrains agricultural productivity in arid and semi-arid regions. This study evaluated exogenous proline as an osmoprotector in Physalis ixocarpa Brot. (Mexican husk tomato) under salinity. Germination screening identified 75 mM NaCl as a threshold stress level, reducing germination by 38.9% while maintaining seedling viability. Proline pretreatment (30-min imbibition) at 8 mM restored germination to 78% and fresh weight to control levels under salt stress. In vitro experiments revealed that 8 mM proline enhanced chlorophyll content above salt-stressed controls while reducing root length from 9.72 to 5.08 cm, indicating resource reallocation toward photosynthetic protection. Infrared spectroscopy showed characteristic polysaccharide shifts and bands potentially associated with proline incorporation. Gas chromatography–mass spectrometry metabolomics of stem–leaf extracts revealed salt-induced synthesis of nitrogenous osmolytes (such as long-chain amines) and carbohydrate reorganization from α-D-glucopyranoside to β-D-riboside. Proline treatment restored the original carbohydrate profile while generating pyrrolidine derivatives (2.83%), evidence of active proline metabolism. Phenolic antioxidants (e.g., catechol) present in controls were absent under both salt stress and proline treatment, suggesting that proline’s protective mechanism may operate through metabolic regulation of osmolyte pathways and membrane stabilization rather than inducing phenolic antioxidant synthesis. These findings demonstrate proline’s multifaceted protective mechanisms and support its potential application for enhancing salt tolerance in this crop.