Abstract Study question Which factors are associated with pre-pregnancy complications and poor well-being in early pregnancy? Summary answer We identified different risk profiles for different pre-pregnancy complications. Besides age and body mass index, exposure to certain prescribed drugs was a modifiable risk factor. What is known already Many couples experience difficulties to become pregnant or carry a pregnancy to term due to unknown causes. Complications including recurrent pregnancy loss (RPL), subfertility (failure to conceive within one year of unprotected intercourse) and the need for artificial reproductive technologies (ART) are increasing worldwide. Previously identified risk factors for involuntary childlessness include higher age, irregular menstruation, endometriosis and polycystic ovary syndrome – however, none of these are modifiable and there are still many cases unexplained. Study design, size, duration Online questionnaires were collected for 5330 unique pregnancies in Sweden from November 2017 – February 2021, collected before 20 weeks of gestation. Participants/materials, setting, methods Participants were defined as having pre-pregnancy complication(s) if they had any of the following: prior RPL (> 3) or late miscarriage, subfertility, or the use of ART. Multivariable logistic regression modelling was used to investigate potential risk factors for pre-pregnancy complications and poor well-being in early pregnancy, reported as odds ratios (OR) with 95% confidence intervals. Main results and the role of chance Pre-pregnancy complications were identified in 1142 participants (21%), with the most common one being subfertility (n = 790, 69%). Risk factors included diagnosed endometriosis (OR 4.43, CI 3.33-5.91), thyroid medication (OR 2.20, CI 1.76-2.74), opioids and other strong pain medication (OR 1.97, CI 1.19-3.19), asthma and allergy medication (OR 1.23, CI 1.03-1.46), body mass index > 25 kg/m2 (OR 1.35, CI 1.07 for BMI 25-29.9 and OR 1.58, CI 1.19-2.07 for BMI ≥ 30) and age over 35 years (OR 1.35, CI 1.07-1.72). Different subgroups of pre-pregnancy complications had unique risk factors. The groups also experienced different symptoms in early pregnancy. Women that had experienced recurrent pregnancy loss were at higher risk of depression during their current pregnancy (OR 1.71, CI 1.21-2.38). All groups were at higher risk for reporting any complications in their current pregnancy (OR 1.33, CI 1.11-1.59), as well as vaginal bleeding (OR 1.72, CI 1.15-2.55). Limitations, reasons for caution We have a high prevalence of participants with RPL, and participants that needed in vitro fertilization (IVF), which indicates a selection bias towards participants with pre-pregnancy complications. Furthermore, we did not collect information on the partner’s medical history, which might play a role in the need for ART. Wider implications of the findings The identified risk factors could be used to identify women at risk for pre-pregnancy complications and help them earlier in the process of trying to conceive, thus assisting them to reduce stress and depression during the pregnancy. Trial registration number Not applicable