Plastoquinone is a key electron carrier in photosynthesis and an essential cofactor for the biosynthesis of carotenoids. p-Hydroxyphenylpyruvate dioxygenase (HPPD) is a vital enzymatic step in plastoquinone biosynthesis that is the target of triketone herbicides, such as those derived from the pharmacophore backbone of the natural product leptospermone. In this work, the inhibitory activity of a series of 2-acyl-cyclohexane-1,3-diones congeners derived from Peperomia natural products was tested on plant HPPD. The most active compound was a 2-acyl-cyclohexane-1,3-dione with a C11 alkyl side chain (5d; I50app: 0.18 ± 0.02 μM) that was slightly more potent than the commercial triketone herbicide sulcotrione (I50app: 0.25 ± 0.02 μM). QSAR analysis and docking studies were performed to further characterize the key structural features imparting activity. A 1,3-dione feature was required for inhibition of HPPD. Molecules with a side chain of 11 carbons were found to be optimal for inhibition, while the presence of a double bond, hydroxy, or methyl beyond the required structural features on the cyclohexane ring generally decreased HPPD inhibiting activity.