Partnership and fertility patterns of young Filipinos have changed dramatically from previous generations, with a widening gap between sexual initiation and marriage, and concurrent increases in teenage pregnancy and unwanted fertility. Further understanding of young adults’ social contexts and partnership patterns are needed to inform reproductive health programmes and policies affecting young Filipinos. Multivariate Poisson regression models were conducted with longitudinal and inter-generational data from the Cebu Longitudinal Health and Nutrition Survey (1998–2009) to examine the predictors of young women’s fertility. Age at first sex, and number and duration of partnerships each independently and significantly predicted women’s fertility by 2009 after controlling for contextual influences. Young women with more conservative attitudes towards dating, sex and marriage, and who perceived their mothers to have more conservative attitudes, had higher fertility than their peers, as did young women with mothers who reported more adolescent sexual behaviours. In contrast, fertility was lower among daughters who had higher levels of communication with their mothers. Given high levels of unintended fertility and teenage pregnancy in the Philippines, the findings indicate that the interval between sexual initiation and first and subsequent partnerships may be ideal intervention points for reproductive health services for young Filipinos.