Graduate students face a variety of barriers when writing manuscripts. The major barrier is inadequate writing experience and training. We aimed to evaluate the awareness and the knowledge of the basic principles in manuscript writing and research integrity among graduate students, and to assess the usefulness of workshops to improve their knowledge about manuscript writing process. A cross sectional survey was developed to evaluate the awareness and the knowledge about the manuscript writing steps and the research integrity among graduate students in Jordan. A one-day workshop about manuscript writing and research integrity was conducted. Students (n = 285) completed the questionnaire. Most participants were female masters’; students. Although 83.8% of the students were aware of the general manuscript structure, most of them were not aware of the basic concepts to write most manuscript sections. Only 22.5% of the students were aware of the authorship criteria. Data showed a lack of knowledge of different practices of scientific misconduct. Barriers in manuscript writing included the lack of focused research methodology courses and the lack of professional workshops and the absence constructive mentorship support. The workshop was useful in introducing the key concepts in manuscript writing. The present study revealed a lack of knowledge among graduate students about manuscript writing and scientific misconduct. Professional workshops are useful in improving students’ knowledge.