A computer-implemented method for managing affinity rules in virtual-machine environments may include (1) identifying a first application configured to run on a first virtual machine, (2) identifying a second application configured to run on a second virtual machine, (3) identifying an application affinity rule between the first application and the second application, the application affinity rule indicating whether the first application and the second application should run on a same hypervisor within a plurality of hypervisors, and (4) selecting, based at least in part on which hypervisor among the plurality of hypervisors is running the first application, a hypervisor from among the plurality of hypervisors on which to run the second application that satisfies the application affinity rule between the first application and the second application. Various other methods, systems, and computer-readable media are also disclosed.