In a chloroplast, the highest number of protons are found in: Stroma, Lumen of thylakoids, Inter-membrane space, Antennae complex

The thylakoid lumen is a continuous aqueous phase, enclosed by the thylakoid membrane. It plays an important role in photophosphorylation during photosynthesis. During the light-dependent reaction, protons are pumped across the thylakoid membrane into the lumen making it acidic down to pH 4. The ATP synthase complex transports protons across the thylakoid from lumen to stroma. These protons flow down an electrochemical gradient and the energy released by that flow is trapped on the stroma side of the thylakoid membrane by ATP synthesis.