Plasmodium falciparum causes the most severe form of malaria and with emerging resistance to frontline antimalarials, there is the need to identify new drug candidates and targets. Nanoluciferase (Nluc) is a highly sensitive and stable luminescent reporter protein that is over 100 fold brighter than its bioluminescent counterparts. Nluc, therefore, provides a powerful tool to utilise in phenotypic screens of drug libraries to discover novel compounds that target the parasite. We set out to identify compounds that inhibit parasite protein export and secretion via screening of the Medicines for Malaria Venture (MMV) Malaria Box. This drug library consists of 400 compounds that exhibit antimalarial properties. To quantify protein export, a parasite line that exported a Nluc reporter into the erythrocyte was utilised. Following drug treatment of the parasites, selective lysis of the parasite, parasitophorous vacuole (PV) and erythrocyte membranes enabled the measurement of Nluc activity in each compartment. This identified 14 compounds that inhibited secretion of protein into the PV. To validate these compounds as secretion inhibitors, 4 compounds were independently sourced and the Nluc assay was repeated. Immunofluorescence microscopy was also used to verify the compounds ability to trap the exported proteins in the parasite. In contrast to the Nluc assay, however, microscopy revealed the compounds failed to trap the exported proteins as expected. To resolve these disparate results, we conducted a counter screen where the compounds were assayed for their ability to directly inhibit Nluc’s bioluminescence activity. All 4 compounds directly Nluc activity, specifically in the buffers used to isolate the erythrocyte and PV compartments. This indicated that the results from the Nluc screen were artifactual. We have therefore identified a subset of the MMV Malaria Box compounds that inhibit Nluc and this has implications for those working with bioluminescence reporters for phenotypic drug screens.