Postharvest events enhance fruit palatability, fragrance and sweetness and reduce sourness. With passion fruit (Passiflora edulis) the underlying molecular events occurring during the postharvest period remain largely unknown. In this study we define how passion fruit flavor alters during the postharvest period using integrated transcriptome and metabolome analyses. Passion fruits were stored under three conditions: room temperature, low temperature, and room temperature with a pre-fumigation with 100 μM methyljasmonate (MeJA). During the postharvest period, organic acid content decreased but sugars and most volatiles increased. While both low temperature and MeJA treatment effectively delayed the aging process, MeJA better maintained fruit flavor. Transcriptomic and network modelling analyses targeted PeWRKY20 was a potential key regulator of the flavor of passion fruit. PeWRKY20 was shown to bind to the Malate Dehydrogenase 1 (PeMDH1) promoter to represses PeMDH1 expression. Transient assays in Nicotiana benthamiana leaves suggested that PeWRKY20 and PeMDH1 function oppositely to regulate the production of malic acid and volatiles, such as heptadecane, dimeththyl phthalate, and L-α-terpineol. Our work unravels a key regulatory hub in postharvest passion fruit development based on an association between malic acid and volatiles.