The species forages over a wide range of habitats, including aquatic habitats, woodland, and farmland, as well as in parks and gardens (reviewed in Rocha 2020). It also feeds near streetlamps (D. Russo pers. obs.). The diet has not been analysed, but prey likely includes moths, small beetles, mosquitos, caddisflies, and flying ants, all caught on the wing. Nursery colonies often roost in wall cracks or under roof tiles but have also been found in bird nest boxes (reviewed in Rocha 2020).

This species is endemic to the European Macaronesian Islands (Spain and Portugal). In the Madeiran Archipelago, it is recorded from across Madeira and Porto Santo, but with only a single record from the Desertas Islands (Teixeira et al. 2023) in Portugal, and from a small number of records in the Azores Archipelago; the identity of pipistrelle bats in the Azores was uncertain, but it was first confirmed on Santa Maria Island based on molecular analysis (Trujillo and González 2011), with very small numbers of records now known from Corvo, Flores, Graciosa, Pico, Santa Maria, and São Jorge islands (Teixeira et al. 2023). In the Canary Islands, it is known from the western Canary Islands of La Palma, La Gomera, El Hierro, and Tenerife (Rocha 2020, Teixeira et al. 2023).

All the recorded islands are regarded as separate locations (13 locations). It is found from sea level to 2,150 m on the Canary Islands, although it prefers lowlands on Madeira (Fajardo and Benzal 1999), where it is known up to 1,500 m asl (Rocha 2020). The AOO was estimated using 2x2 km grid cells.

Pipistrellus maderensis is protected by national legislation in Portugal and Spain as well as by the Eurobats Agreement and Bern Convention. It is included in Annex IV of the EU Habitats Directive. It is one of the Eurobats' priority species for autoecological studies since very little is known about its ecology and even distribution and population size and trends. This species requires basic research to inform management, including distribution, a genetic assessment of subpopulations on the different islands, population size and trends, spatial ecology, and diet. Protection of roosting sites as well as known foraging habitats is paramount to preserving P. maderensis.