Cape gooseberry has coped with abiotic and biotic stresses such as prolonged waterlogging periods and vascular wilt in recent years. The aim of this study was to evaluate the influence of four waterlogging periods on stomatal conductance (gs), leaf water potential (Ψwf), plant growth, leaf photosynthetic pigments, malondialdehyde (MDA) production, proline content and chlorophyll fluorescence parameters in cape gooseberry plants infected with Fusarium oxysporum f. sp. physali (Foph). Two-month-old ecotype “Colombia” plants were arranged in a completely randomized factorial design in eight treatments: plants without waterlogging (control), plants with waterlogging for 4, 6 and 8 d with and without Foph, respectively. The area under the disease progress curve was higher in inoculated plants subjected to 6 and 8 d of waterlogging (55.25 and 64.25) compared to inoculated plants but without waterlogging (45.25). The results also showed a lower plant growth, gs, Ψwf, leaf photosynthetic pigments and chlorophyll fluorescence parameters (Fv/Fm, electron transport rate (ETR), Y (II) and qP) as waterlogging periods in plants with Foph increased. However, this group of plants showed a greater proline and malondialdehyde (MDA) accumulation and a higher NPQ. In conclusion, cape gooseberry shows a low acclimation to waterlogging conditions of more than 6 d in soils with Foph.