Over the past 20 years, significant effort has been devoted to advancing the modular approach to teaching chemistry laboratory courses. The development and implementation of two modules are presented here for teaching a second-semester physical chemistry laboratory course using the modular approach: an inquiry-based module concerning proteins and a project-based module concerning organic small molecules. Each module focuses on a molecular system in question and allows participating students to choose and apply various methods to study the system in different ways, according to the advantages and disadvantages of each method. The common thrust of all of the modules is to develop students' critical thinking skills, provide them a conduit to apply their knowledge to real applications, encourage them to model the approaches and behavior of practicing scientists, and excite them to initiate and pursue research opportunities. Details of implementation of this modular approach in teaching the second-semester physical chemistry laboratory for the past 11 years are provided. The assessment results indicate encouraging evidence that this two-level modular approach has achieved its goals and assisted students in choosing more research-based careers.