Cellulose is the strongest cell wall polymer defining plant cell shape and growth, and the most abundant biopolymer on the Earth. Its synthesis by the plasma membrane (PM)-localized cellulose synthase complexes (CSCs) depends on surrounding lipids that establish the membrane microenvironment in which CSCs work and form vesicles delivering and removing CSCs to and from the PM by exo- and endocytosis. The role of exact lipid molecular species in these processes is poorly understood. In the present work we used hypocotyls of etiolated wild-type Col-0 and mutant ixr1-1 Arabidopsis thaliana seedlings grown with or without isoxaben, a specific cellulose synthesis inhibitor, as a model to reveal lipid molecular species associated with cellulose biosynthesis. Different lipid classes were separated by thin-layer chromatography (TLC) and their molecular species were analyzed by liquid chromatography–triple quadrupole tandem mass spectrometry (LC-QqQ-MS/MS). A total of 250 lipid molecular species were identified. Col-0 plants maintained stable levels of membrane glycerophospholipids but displayed significant remodeling of their acyl chains. In the presence of isoxaben, they accumulated three times more phosphatidic acids, a hallmark of a stress response. The isoxaben-resistant mutant ixr1-1 was characterized by a higher relative content of phosphatidylethanolamines, potentially rendering membranes more labile, as well as plastid galactolipids, which accumulated under isoxaben treatment. The multifaceted effects of isoxaben, including its impact on endomembrane lipids, suggest that it has additional binding sites beyond CSC.