Weed management can be difficult and expensive in organic agricultural systems. Because of the potentially high cost of the natural product herbicides vinegar and clove oil, their efficacy with regard to weed species growth stages needs to be determined. A further objective was to identify anatomical and morphological features of redroot pigweed and velvetleaf that influence the effectiveness of vinegar and clove oil. Research was conducted on greenhouse-grown cotyledon, two-leaf, and four-leaf redroot pigweed and velvetleaf. Dose–response treatments for vinegar included 150-, 200-, 250-, and 300-grain vinegar at 318 L/ha and at 636 L/ha. Clove oil treatments included 1.7, 3.4, 5.1, and 6.8% (v/v) dilutions of a clove oil product in water (318 L/ha), and a 1.7% (v/v) dilution in 200-grain vinegar (318 L/ha). An untreated control was included. Separate plantings of velvetleaf and pigweed were treated with vinegar or clove oil and were used to study anatomical and morphological differences between the two species. Redroot pigweed was easier to control with both products than velvetleaf. Whereas 200-grain vinegar applied at 636 L/ha provided 100% control (6 d after treatment [DAT]) and mortality (9 DAT) of two-leaf redroot pigweed, this same treatment on two-leaf velvetleaf provided only 73% control and 18% mortality. The obtuse leaf blade angle in velvetleaf moved product away from the shoot tip, whereas in pigweed, the acute leaf blade angle, deep central leaf vein, and groove on the upper side of the leaf petiole facilitated product movement toward the stem axis and shoot tip. For both species, and at all application timings, 150-grain vinegar at 636 L/ha provided control equal to that of 300-grain vinegar at 318 L/ha. As growth stage advanced, control and biomass reduction decreased and survival increased. Application timing will be critical to maximizing weed control with vinegar and clove oil.