Optimal operation and control of heat recovery in an integrated Laboratory Air Handling Unit (LAHU) system differs substantially from that in conventional dedicated AHUs for laboratory buildings with a 100% outside air AHU for laboratory spaces, since the LAHU allows economizer operation for both offices and laboratories. Optimal operation and control schedules of the heat recovery systems in the LAHU have been developed to minimize the total thermal energy cost. This paper presents the procedure, methodology, and results of generic optimal heat recovery control schedules for the LAHU and investigates its impact on the LAHU potential thermal and pump energy savings. The optimal control schedule can potentially save 14% to 27% thermal energy and 17% to 100% pump energy during the winter under weather conditions that prevail in Omaha, Nebraska. The findings discussed in this paper also apply to any heat recovery system, where AHU has an economizer function.