Ramsey rootstock has previously been implicated in an approximate 8-fold increase of 3-isobutyl-2-methoxypyrazine (IBMP) levels in the rachis (grape bunch stem) of Vitis vinifera L. cv. Shiraz scions over own-rooted Shiraz vines at harvest. IBMP extracted from rachis during red wine fermentation can contribute potent “green” flavors. Methoxypyrazines (MPs) are normally present in Cabernet Sauvignon grapes, rachis, and wines, but it is unknown whether rootstocks can influence the MP concentration in the rachis. This study considered the effect of eight rootstocks including Ramsey and own roots on the concentrations of IBMP, 3-isopropyl-2-methoxypyrazine (IPMP), and 3-sec-butyl-2-methoxypyrazine (SBMP) in the rachis and grapes of Cabernet Sauvignon over two seasons. IBMP predominated, and its concentration in rachis and berries at harvest was significantly affected by rootstock and growing season. In the 2020 vintage, light exclusion, vine vigor, and spatial variation in vine vigor were shown to significantly affect MP concentrations in rachis.