The protein productions strategies are crucial towards the development of application based research and elucidating the novel purification strategies for industrial production. Currently， there are few innovative avenues are studies for cloning， upstream， and purification through efficient bioprocess development. Such strategies are beneficial for industries as well as proven to be vital for effectual therapeutic protein development. Though， these techniques are well documented， but， there is scope of addition to current knowledge with novel and new approaches and it will pave new avenues in production of recombinant microbial and non-microbial proteins including secondary metabolites. In this review， we have focussed on the recent development in clone selection， various modern fermentation and purification technologies and future directions in these emerging areas. Moreover， we have also highlighted notable perspectives and challenges involved in the bioengineering of such proteins， including quality by design， gene editing and pioneering ideas. The biopharmaceutical industries continue to shift towards more flexible， automated platforms and economical product development， which in turn can help in developing the cost effective processes and affordable drug development for a large community.