Under the guidance of Joseph Barth (1745–1818), his primary focus turned to the field of ophthalmology.

The final break in their relationship was caused by Barth's favour of Johann Adam Schmidt (1759–1809), who later became a renowned ophthalmologist.

Eventually he built a successful practice despite the obstacles created by Barth, who publicly expressed doubts in regard to Beer's qualifications.

Beer became a popular teacher, and attracted a number of students who later excelled in the field of ophthalmology.

His best written work was the celebrated Lehre von den Augenkrankheiten, als Leitfaden zu seinen öffentlichen Vorlesungen entworfen, which was used as an important reference in ophthalmic medicine for many years afterward.