The woman, who has not yet been publicly named, had not been in contact with friends or relatives since October 2017 although she was only reported missing by her family in December.
Police said the delay was explained because there was often periods of non-contact between the woman and family members.
On Thursday, investigators received a warrant to search the property where the couple lived and then made the grim discovery.
Her body, which had been chopped into pieces, was found in a chest freezer in the bathroom, according to police sources quoted by Spanish news agency EFE.
Her boyfriend was arrested around 4.30am on Friday.
Detenido el presunto autor del homicidio de una mujer hallada muerta en su domicilio en #Alcalá de Henares.
— Policía Nacional (@policia) February 8, 2019
If her murder is confirmed to be a case of domestic violence, it will be the eighth murder at the hands of a partner or ex-partner so far reported in 2019.
According to official statistics, since 2003, which is when such records began, 983 women have been murdered in domestic violence cases in Spain.
Cases of children being killed as a result of domestic violence began to be recorded in 2013, and since then 27 minors have been killed while 225 have lost their mothers.