Background: Intestinal schistosomiasis MESHD was not considered endemic in Lake Malawi until November 2017 when populations of Biomphalaria pfeifferi were first reported; in May 2018, emergence of intestinal schistosomiasis MESHD was confirmed. This emergence was in spite of ongoing control of urogenital schistosomiasis MESHD by preventive chemotherapy. Our current study sought to ascertain whether intestinal schistosomiasis MESHD is transitioning from emergence to outbreak, to judge if stepped-up control interventions are needed.Methods: During late-May 2019, three cross-sectional surveys of primary school children TRANS for schistosomiasis MESHD were conducted using a combination of rapid diagnostic tests, parasitological examinations and applied morbidity-markers; 1) schistosomiasis MESHD dynamics were assessed at Samama (n = 80) and Mchoka (n = 80) schools, where Schistosoma mansoni was first reported, 2) occurrence of S. mansoni was investigated at two non-sampled schools, Mangochi Orphan Education and Training (MOET) (n = 60) and Koche (n = 60) schools, where B. pfeifferi was nearby, and 3) rapid mapping of schistosomiasis MESHD, and B. pfeifferi, conducted across a further 8 shoreline schools (n = 240). After data collection, univariate analyses and Chi-square testing were performed, followed by binary logistic regression using generalized linear models, to investigate epidemiological associations.Results: In total, 520 children TRANS from 12 lakeshore primary schools were examined, mean prevalence SERO of S. mansoni by ‘positive’ urine circulating cathodic antigen (CCA)-dipsticks was 31.5% (95% Confidence Interval (CI): 27.5–35.5). Upon comparisons of infection MESHD prevalence SERO in May 2018, significant increases at Samama (Relative Risk (RR) = 1.7, 95% CI: 1.4–2.2) and Mchoka (RR = 2.7, 95% CI: 1.7–4.3) schools were observed. Intestinal schistosomiasis MESHD was confirmed at MOET (18.3%) and Koche (35.0%) schools, and in all rapid mapping schools, ranging from 10.0% to 56.7%. Several populations of B. pfeifferi were confirmed, with two new eastern shoreline locations noted. Mean prevalence SERO of urogenital schistosomiasis MESHD was 24.0% (95% CI: 20.3–27.7). Conclusions: We notify that intestinal schistosomiasis MESHD, once considered non-endemic in Lake Malawi, is now transitioning from emergence to outbreak. Once control interventions can resume after coronavirus disease MESHD 2019 (COVID-19) suspensions, we recommend stepped-up preventive chemotherapy, with increased community-access to treatments, alongside renewed efforts in appropriate environmental control.