Covert contraceptive use is a strategy to avoid unintended pregnancy. However, evidence regarding the multilevel factors linking past experiences of unintended pregnancy with covert contraceptive use is limited. The objective of this study was to identify the compositional and contextual factors associated with covert contraceptive use among women with a prior unintended pregnancy. Framed by the socio-ecological model, a cross-sectional study was conducted using data from Round 5 of the Performance Monitoring and Accountability 2020 project in Nigeria. Non-pregnant women aged 15–49 years who reported a previous mistimed or unwanted pregnancy were included (N = 1631). Multilevel logistic regression models with random intercepts were specified to investigate the relationship between covert contraceptive use and compositional and contextual factors. Approximately 4.54% (95% CI = 3.28–6.25) of women reported covert contraceptive use. At the individual level, having less than secondary education (aOR = 5.88, 95% CI = 1.20–28.72) and being single (aOR = 11.29, 95% CI = 2.93–43.56) were associated with higher odds of covert contraceptive use. There was no significant association between covert contraceptive use and the type of unintended pregnancy (mistimed: aOR = 3.13, 95% CI = 0.88–11.13). At the community level, living in a community with average poverty levels (aOR = 6.18, 95% CI = 1.18–32.55) and high exposure to family planning mass media (aOR = 6.84, 95% CI = 1.62–29.11) were associated with higher odds of covert contraceptive use. Measures of variation showed significant variation in covert contraceptive use across communities. Further research is warranted to better understand the underlying mechanisms in these observed associations and variations in covert contraceptive use among women following the experience of an unintended pregnancy. Additionally, there is a need to design family planning strategies that integrate community-level structures.