This study investigated the implementation of best teaching practices by science graduate teaching assistants [GTAs] (3 chemists and 2 biologists) in five inquiry-based, interdisciplinary chemistry-biology experiments during a six-week professional development (PD) program, Engage PD. Additionally, we examined GTAs' experiences in implementing specific PD aspects. The PD program took place as the GTAs taught sections of biology and chemistry laboratory courses, each comprising five interdisciplinary experiments. The PD aspects included defining expected learning outcomes, subject-matter knowledge, relevance to real-world and chemistry-biology connections, and other active classroom teaching practices. Data were collected through classroom observations, reflection questionnaires, and individual interviews. Findings indicated that 57% of the PD aspects investigated were implemented in the five interdisciplinary experiments. Results also revealed GTAs' initial areas of struggle in implementing specific PD aspects. Perceived implementation difficulties were attributed to individual perceptions and beliefs, and contextual factors. Through practice, continuous feedback, and reflections, most GTAs overcame the hurdles and refined their teaching. Findings imply the need to design training PD programs that offer mentoring and support to GTAs and future faculty in implementing teaching innovations. The teaching context and reflection prompts are helpful in identifying areas of difficulties and how to improve.