Semiconductor devices having multiple substrates and die stacks, and associated systems and methods, are disclosed herein. In some embodiments, a semiconductor device includes a package substrate, and a first die stack mounted on the package substrate and including a plurality of first memory dies. The device can include a substrate mounted on the first die stack, the substrate including a plurality of routing elements. The device can also include a second die stack mounted on the substrate, the second die stack including a plurality of second memory dies. The device can further include a controller die mounted on the substrate. The controller die can be configured to communicate with the second die stack via the routing elements of the substrate. The device can include a mold material encapsulating the first die stack, the second die stack, the substrate, and the controller die.