Recent basaltic-andesite lavas from Merapi volcano contain abundant and varied igneous inclusions suggesting a complex sub-volcanic magmatic system for Merapi volcano. In order to better understand the processes occurring beneath Merapi, we have studied this suite of inclusions by petrography, geochemistry and geobarometric calculations. The inclusions may be classified into four main suites: (1) highly crystalline basaltic-andesite inclusions, (2) co-magmatic enclaves, (3) plutonic crystalline inclusions and (4) amphibole megacrysts. Highly crystalline basaltic-andesite inclusions and co-magmatic enclaves typically display liquid-liquid relationships with their host rocks, indicating mixing and mingling of distinct magmas. Co-magmatic enclaves are basaltic in composition and occasionally display chilled margins, whereas highly crystalline basaltic-andesite inclusions usually lack chilling. Plutonic inclusions have variable grain sizes and occasionally possess crystal layering with a spectrum of compositions spanning from gabbro to diorite. Plagioclase, pyroxene and amphibole are the dominant phases present in both the inclusions and the host lavas. Mineral compositions of the inclusions largely overlap with compositions of minerals in recent and historic basaltic-andesites and the enclaves they contain, indicating a cognate or 'antelithic' nature for most of the plutonic inclusions. Many of the plutonic inclusions plot together with the host basaltic-andesites along fractional crystallisation trends from parental basalt to andesite compositions. Results for mineral geobarometry on the inclusions suggest a crystallisation history for the plutonic inclusions and the recent and historic Merapi magmas that spans the full depth of the crust, indicating a multi-chamber magma system with high amounts of semi-molten crystalline mush. There, crystallisation, crystal accumulation, magma mixing and mafic recharge take place. Comparison of the barometric results with whole rock Sr, Nd, and Pb isotope data for the inclusions suggests input of crustal material as magma ascends from depth, with a significant late addition of sedimentary material from the uppermost crust. The type of multi-chamber plumbing system envisaged contains large portions of crystal mush and provides ample opportunity to recycle the magmatic crystalline roots as well as interact with the surrounding host lithologies. © 2012 Springer-Verlag.