In Modern Mongolian, the subjects of many subordinate clauses, both complements and adjuncts, may be marked with the accusative case (von Heusinger, Klein & Guntsetseg 2011; Guntsetseg 2016). This study argues that the full empirical picture of these marked subjects necessitates an analysis based on Dependent Case Theory (Marantz 1991; Baker & Vinokurova 2010; Baker 2015), which additionally provides an account of case assignment more broadly in the language, including in differential object marking. Prior syntactic analyses (Bao et al. 2015; Fong 2019) rely on Agree-based case-licensing from v, resulting in ECM-like accounts. However, the appearance of accusative on subjects of adjoined clauses, as well as in clauses with no canonical accusative-assigning verbs (intransitives, passives) rules out v as the case assigner. Instead, following Baker & Vinokurova (2010), this account argues that accusative case is assigned configurationally. Once established that a configurational approach to case-assignment handles subjects, as well as direct objects, the approach is applied to Mongolian-specific issues including voice alternations and converbial adjuncts, showing that the theory predicts case-assignment patterns there. Finally, the study examines data from dative marking and scrambling in ditransitives to refine Baker & Vinokurova’s (2010) original theory, obviating the need for case-stacking by restricting the timing of application of the Dependent Case algorithm.