An integrated pharmaceutical processing system comprising: a lyophilizing subsystem configured to lyophilize a pharmaceutical substance and having a lyophilizer interior chamber sealable from an ambient environment and a supply portal with a sealable door; and a lyophilizer loading subsystem having a loader interior chamber sealable from the ambient environment and in communication with the lyophilizer interior chamber via the supply portal, the loading subsystem comprising within the loader interior chamber: a multi-nest support mechanism that includes a plurality of support structures that are each constructed to support one of a plurality of multi-container nests, and having a range of motion that extends between a nest loading station and a first location in the lyophilizer interior chamber, the multi-nest support mechanism also including an articulated robotic arm configured to engage simultaneously with the plurality of multi-container nests and to place them via the supply portal at a first location in the lyophilizer interior chamber, wherein the articulated robotic arm comprises a rotary end effector disposed at a distal end of the articulated robotic arm, wherein the rotary end effector includes the multi-nest support mechanism on a first side and a pushing surface on a second side; and a drive mechanism operatively connected to the multi-nest support mechanism and operative to drive the multi-nest support mechanism between the nest loading station and the first location in the lyophilizer interior chamber. a lyophilizing subsystem configured to lyophilize a pharmaceutical substance and having a lyophilizer interior chamber sealable from an ambient environment and a supply portal with a sealable door; and a lyophilizer loading subsystem having a loader interior chamber sealable from the ambient environment and in communication with the lyophilizer interior chamber via the supply portal, the loading subsystem comprising within the loader interior chamber: a multi-nest support mechanism that includes a plurality of support structures that are each constructed to support one of a plurality of multi-container nests, and having a range of motion that extends between a nest loading station and a first location in the lyophilizer interior chamber, the multi-nest support mechanism also including an articulated robotic arm configured to engage simultaneously with the plurality of multi-container nests and to place them via the supply portal at a first location in the lyophilizer interior chamber, wherein the articulated robotic arm comprises a rotary end effector disposed at a distal end of the articulated robotic arm, wherein the rotary end effector includes the multi-nest support mechanism on a first side and a pushing surface on a second side; and a drive mechanism operatively connected to the multi-nest support mechanism and operative to drive the multi-nest support mechanism between the nest loading station and the first location in the lyophilizer interior chamber. a multi-nest support mechanism that includes a plurality of support structures that are each constructed to support one of a plurality of multi-container nests, and having a range of motion that extends between a nest loading station and a first location in the lyophilizer interior chamber, the multi-nest support mechanism also including an articulated robotic arm configured to engage simultaneously with the plurality of multi-container nests and to place them via the supply portal at a first location in the lyophilizer interior chamber, wherein the articulated robotic arm comprises a rotary end effector disposed at a distal end of the articulated robotic arm, wherein the rotary end effector includes the multi-nest support mechanism on a first side and a pushing surface on a second side; and a drive mechanism operatively connected to the multi-nest support mechanism and operative to drive the multi-nest support mechanism between the nest loading station and the first location in the lyophilizer interior chamber.