Scientific output in health sciences has grown exponentially, yet its landscape remains under-analyzed in emerging economies. In Peru, Microbiology and Parasitology are disciplines of strategic relevance for public health, but no specific bibliometric analysis exists. This study provides the first baseline to identify thematic gaps and characterize research patterns within the SciELO Peru collection. Through a descriptive bibliometric analysis of 549 Microbiology and Parasitology articles indexed in the SciELO Peru collection (2000–2023), temporal, regional, and institutional indicators, methodological design, and journal characteristics were evaluated using R v4.4.0. Results show that production peaked in 2021, coinciding with the COVID-19 pandemic period and accompanied by a marked increase in Virology-related publications. Lima accounted for 77.3% of the SciELO Peru corpus national output, with UPCH (17.5%), INS (14.9%), and UNMSM (13.7%) leading institutional activity. Bacteriology was the dominant area (44.1%), while Mycology was the most underrepresented (2.4%), and cross-sectional designs predominated (63.9%). Notably, real international collaboration was limited to 1.8%, and RPMESP was the sole Bradford core journal, accounting for 48.5% of the corpus, with no articles appearing in Q1 journals. These findings reveal that while production shows sustained growth, it is marked by high geographic concentration and a scarcity of applied technological research within the analyzed corpus. These findings highlight the urgent need to decentralize research and reorient Peru’s health science agenda toward critical, under-studied disciplines.