Metal-organic frameworks (MOFs) are very promising host materials for nanoscale guest materials. However, some MOFs such as MIL-53 are known to undergo phase transitions which can complicate the guest particle size control. In this study, Pd nanoparticles embedded in Al-MIL-53 were synthesised via (a) electrodeposition and (b) gas-phase reduction. A thorough structural investigation revealed that each synthesis method most likely favoured a different phase of Al-MIL-53, presenting the possibility of MOF phase selection as a technique for size control of embedded nanoparticles. For the first time, we hereby report the use of pair distribution function analysis to successfully investigate the structure and morphology of guest particles embedded in a MOF host.