The search for structurally relevant Al-arrangements in zeolites is an important endeavor for single site catalysis. Little is known about the mechanisms and zeolite dynamics during synthesis that are responsible for creating those Al-ensembles. Here, new synthetic strategies for creating Al-hosts in small-pore zeolites suitable for divalent cation catalysis are uncovered, leading to a mechanistic proposal for Al-organization during crystallization. As such, unique synthesis-structure-activity relations are demonstrated for the partial oxidation of methane on Fe-exchanged CHA-zeolites. With modified interzeolite conversions, the divalent cation capacity of the resulting high Si SSZ-13 zeolites (Si/Al ~ 35) can be reproducibly controlled in a range between 0.04 and 0.34 Co²⁺/Al. This capacity is a proxy for the distribution of framework aluminum in pairs and correlates with the methanol production per Al when these zeolites host the α-Fe^(II) redox active site. The uncovered IZC synthesis-structure relations paint an Al-distribution hypothesis, where incongruent dissolution of the starting USY zeolite and fast synthesis kinetics with atypical growth modes allow assembling specific Al-arrangements, resulting in a high divalent cation capacity. Prolonged synthesis times and high temperatures overcome the energetic barriers for T-atom reshuffling favoring Al-isolation. These mechanisms and the relations uncovered in this work will guide the search for relevant Al-ensembles in a range of zeolite catalysts where controlling the environment for a single active site is crucial
