Warehouses play an important value-adding role to provide a competitive edge, support business growth and efficiency throughout their supply chains. This paper explores warehouse operations (i.e. receiving, put away, picking, packing and shipping) and a series of challenges faced in managing warehouse operations in general and the 3PL industry in particular. Especially, the paper analyses the warehouse and logistics operations of an Australian 3PL company. By utilizing a mixed method approach both qualitative and quantitative data was gathered through indepth interviews, direct observations and warehouse operations records. The collected data were then analyzed using thematic analysis. The data was screened and coded to further develop major themes to identify the problematic areas. This analysis helped to identify issues in operations related to the receiving process, missing, picking and locating items as well as human errors. While multiple approaches could be utilized to improve the operations, there yet remained a major challenge to manage operations within the planned budgetary limits. This research, therefore, provides some solutions/recommendations to improve the case company's warehouse operations through staff empowerment, management process improvement, order dispatch and return process improvement, improvement in record keeping, and recruiting more personnel. These recommendations ensure company's efficiency while balancing its challenges both in operations and budgetary constraints. This study thus provides an evidence to improve the reliability of warehouse operations through systematic process improvement.