Background Pharmacists are crucial in lowering pharmaceutical expenditures by substituting brand-name drugs for generic drugs. They are expected to understand the principles and practices of generic drug substitution for high-quality patient care. Some key areas of knowledge include bioequivalence and therapeutic equivalence, regulatory requirements, drug interchangeability, and adequate patient counseling. Objectives This study aims to assess the knowledge, perception, and practice of generic drug substitution among pharmacists in Lebanon following the crises and the factors affecting the prescription and selection of generic drugs. Methods A pilot descriptive cross-sectional study targeting 80 Lebanese pharmacists was conducted over 2 months (September-October 2022), in which data were collected using a uniform survey. Results Overall, pharmacists had a good knowledge of generic drugs in terms of active ingredients (97.5%), pharmaceutical form (85.0%), lower cost (88.7%), bioequivalence to the brand before (95.0%), and therapeutic equivalence. Nevertheless, 22.5% reported that generic drugs are less safe than brands, and 22.5% said they cause side effects or did not know. Among the possible factors that influence the prescription of generic drugs, 35.0% of pharmacists reported that the financial situation of the patient is among the least important factors, while the lack of possible alternatives (45.0%) and the difference in prices (40.0%) were the most important ones. The price of different generics on the market was among the most important factors (36.3%) affecting the selection of generic drugs, followed by the patient’s. preference (26.3%). Only 11.2% considered the information given by pharmaceutical firms could affect their choice, and 10.0% considered the presence or not of excipients with known effects in the formulation. Conclusion Most pharmacists in Lebanon were familiar with generic drugs and supported generic drug substitution. Factors affecting generic drug use and prescription should be further explored to clarify misconceptions and reduce possible adverse events.