To address these points, this study presents a versatile, one-pot hydrothermal synthesis approach to simultaneously control MoS2 crystallite size by pH adjustment, interlayer distance by the use of alkylamine organic pillars, and interlayer composition by varying pillar concentration. Organic pillars are interchangeable allowing to widely tune MoS2 nanoconfinement chemistry via this approach. Comprehensive structural investigation reveals the resulting morphology and crystallography as a function of synthesis parameters and clarifies the interaction between MoS2 host and alkylamine pillars. Electrochemical lithium intercalation properties are conclusively linked to the MoS2 structure, with pseudocapacitive intercalation properties being amplified for smaller crystallites, larger interlayer distances and reduced pillar concentration. While we demonstrate the viability of our materials for lithium intercalation, the findings may be of broader relevance. Crystallite size and/or interlayer engineering of TMDs are considered critical for, among others, intercalation of multivalent ions, metal ion adsorption for water purification, or electrocatalytic hydrogen evolution .